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VOLUME 6 NUMBER 2 JUNE 2008
(Sponsored by Ministry of Environment and Forests, Government of India)(Sponsored by Ministry of Environment and Forests, Government of India)
ENVIS NEWSLETTERENVIS NEWSLETTERMICROORGANISMS AND ENVIRONMENT MANAGEMENTMICROORGANISMS AND ENVIRONMENT MANAGEMENT
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ISSN-0974-1550
Volume 6 | Number 2 | June 2008
EDITORS Prof. N. Munuswamy
(ENVIS Co-ordinator)
Dr. N. Godhantaraman
Scientist - D
ENVIS TEAM
Prof. N. Munuswamy (Co-ordinator)
Dr. N. Godhantaraman (Scientist - D)
Mr.S. Padmanabhan (Information Officer)
Mrs. N. Vijaya Lakshmi (Asst. Information Officer)
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Environmental Information System (ENVIS)
Cover Page : Fungus (Pleurotus sp.)
ENVIS Newsletter on Microorganisms and Environment Management
VOLUME 6 NUMBER 2 JUNE 2008
ENVIS CENTRE Newsletter Vol.6, No.2 June 2008
Dear Readers,
Thanks for your readership. Once again
we bring to you our quarterly ENVIS Newsletter on
“ M i c r o o r g a n i s m s a n d E n v i r o n m e n t
Management”.
Along with research articles, reports and
abstracts of recent publications, this issue also
highlights the significance of ‘World Environment
Day 2008’.
th On 5 June 2008, the fraternity at the
Guindy Campus, University of Madras came
together to show their commitment to save the
earth - planet. They pledged to “Kick the Habit”
(the ‘carbon’ habit) and organised a campus
cleaning drive. Saplings were planted in the
campus and the commitment to be a part of the
solution towards a carbon-neutral existence was
reinforced.
ENVIS newsletter has become a popular
source of informat ion on environment
management and related issues. We appreciate
your constructive feedback to improve our
activities and services.
For further information about ENVIS, please
visit : http://www.envismadrasuniv.org
World Environment Day, Message from UN
Secretary General
SCIENTIFIC ARTICLES
Environmental Degradation of Polyolefin's Ambika Arkatkarand Mukesh Doble
Decolourization of Effluent using Immobilized
Fungus (Pleurotus sp. MAK-II)
M. Arulmani, K. Murugesan, V. Geetha and
P.T. Kalaichelvan
Prospects of Marine Biofertilizers for Saline
Soil Crop Cultivation
S. Ravikumar
RESEARCH REPORTS
Abundance and Diversity of Microbial life in
Ocean Crust
ONLINE REPORTS ON MICROORGANISMS
Seafloor Diversity Points to Origin of Life
Microbes Mutated in Outer Space become far
more Dangerous
Microbes as Climate Engineers
Methane from Microbes a Fuel for the Future
NEWS
Rain - Making Bacteria found Worldwide
MEETING REPORT
Summer Workshop on Fungal Biotechnology
ABSTRACTS OF RECENT PUBLICATIONS
IMPORTANT E-RESOURCES ON
MICROORGANISMS
EVENTS
Contents
Prof. N. Munuswamy
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Page No.
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2
MESSAGE FOR WORLD ENVIRONMENTAL DAY 2008
A
ENVIS CENTRE Newsletter Vol.6, No.2 June 2008
ddiction is a terrible thing. It consumes and controls us, makes us deny important truths and blinds us to the consequences of our actions. Our world is in the grip of a dangerous carbon habit.
Coal and oil paved the way for the developed world’s industrial progress. Fast-developing countries are now taking the same path in search of equal living standards. Meanwhile, in the least developed countries, even less sustainable energy sources, such as charcoal, remain the only available option for the poor.
Our dependence on carbon-based energy has caused a significant build-up of greenhouse gases in the atmosphere. Last year, the Nobel Peace Prize-winning Intergovernmental Panel on Climate Change put the final nail in the coffin of global warming sceptics. We know that climate change is happening, and we know that carbon dioxide and other greenhouse gases that we emit are the cause.
We don’t just burn carbon in the form of fossil fuels. Throughout the tropics, valuable forests are being felled for timber and making paper, for pasture and arable land and, increasingly, for plantations to supply a growing demand for biofuels. This
; further manifestation of our carbon habit not only releases vast amounts of CO it also destroys a valuable resource for absorbing 2
atmospheric carbon, further contributing to climate change.
The environmental, economic and political implications of global warming are profound. Ecosystems -- from mountain to ocean, from the Poles to the tropics -- are undergoing rapid change. Low-lying cities face inundation, fertile lands are turning to desert, and weather patterns are becoming ever more unpredictable.
The cost will be borne by all. The poor will be hardest hit by weather-related disasters and by soaring price inflation for staple foods, but even the richest nations face the prospect of economic recession and a world in conflict over diminishing resources. Mitigating climate change, eradicating poverty and promoting economic and political stability all demand the same solution: we must kick the carbon habit. This is the theme for World Environment Day 2008. “Kick the Habit: Towards a Low Carbon Economy”, recognizes the damaging extent of our addiction, and it shows the way forward.
Often we need a crisis to wake us to reality. With the climate crisis upon us, businesses and governments are realizing that, far from costing the Earth, addressing global warming can actually save money and invigorate economies. While the estimated costs of climate change are incalculable, the price tag for fighting it may be less than any of us may have thought. Some estimates put the cost at less than one per cent of global gross domestic product -- a cheap price indeed for waging a global war.
Even better news is that technologies already exist are under development to make our consumption of carbon-based fuels cleaner and more efficient and to harness the renewable power of sun, wind and waves. The private sector, in particular, is competing to capitalize on what they recognize as a massive business opportunity.
Around the world, nations, cities, organizations and businesses are looking afresh at green options. At the United Nations, I have instructed that the plan for renovating our New York headquarters should follow strict environmental guidelines. I have also asked the chief executives of all UN programmes, funds and specialized agencies to move swiftly towards carbon neutrality.
Earlier this year, the UN Environment Programme launched a climate neutral network -- CN Net -- to energize this growing trend. Its inaugural members, which include countries, cities and companies, are pioneers in a movement that I believe will increasingly define environmental, economic and political discourse and decision making over the coming decades.
The message of World Environment Day 2008 is that we are all part of the solution. Whether you are an individual, an organization, a business or a government, there are many steps you can take to reduce your carbon footprint. This message we all must take to heart.
Mr. Ban Ki-MoonSECRETARY-GENERAL OF UNITED NATIONS
“KICK THE CARBON HABIT”
History
n India according to future flow analysis the total
virgin plastics consumption is expected to reach
20,000 KT by the year of 2030 and over 18, 800 KT of
waste can be generated. The consumption of
thermoplastics was 40 million tones in European
countries (Plastemart.com website, 2004 & 2006).
Polyolefins like Polypropylene (PP), Low density
polyethylene (LDPE) & High density polyethylene
(HDPE) account for about 60% of the total plastics
consumption in India. Dumping of plastic in the
environment at such a large amount is causing already
serious problems to the flora and fauna. The
conventional method like incineration is a source of
secondary hazardous product. This plastic waste
degrades the environmental conditions at a very slow
rate. The low rate of biodegradation of plastics is
usually due to properties of the polymeric material like
lack of water solubility (Hydrophobicity) and size of the
polymer molecules (long chains and high molecular
weight which prevents the breakdown of the polymeric
bond) that microbial cell are unable to transport directly
in their cells.
Literature review
Biodegradation ultimately results in the
consumption of polymer by the microorganism. The
growth activity study of the microbes like fungi
(Aspergillus niger, A.flavus, A.oryzae, Chaetomium
globusum, Penicillium funiculosum, Pullularia
pullulan), bacteria (Pseudomonas aeruginosa,
Bacillus cereus,
Coryneformes bacterium, Mycobacterium, Nocardia,
Corynebacterium and Candida) and Actinomycetales
(Streptomycetaceae) on the agar plate for a definite
Pseudomonas sp., Bacillus sp.,
time period revealed the capability of these
microbes to degrade. Polyethylene (PE). There are
scare reports on PP biodegradation. Fungal species
(A. niger) and microbial communities such as
Pseudomonas and Vibrio species have been
reported to biodegrade PP. Isotactic PP exposed to
a bacterial consortium for 175 days had 40%
methylene chloride extractable compounds, which
was mixture of hydrocarbons (between C H to 10 22
C H ). 30-60 % growth of A. niger was observed on 31 64
gamma irradiated PP films in six weeks, indicating
that the fungus is able to grow taking this polymer as
its sole carbon source. The continuous chain of
repetitive methylene units makes PP resistant to
degradation.
How to address the problem?
For achieving the task of biodegradation it is a
prerequisite that the polymer surface is modified to
some extent. Pretreatment and blending PE with
natural polymer can modify the surface.
Pretreatments
Under environmental conditions natural
weathering, which includes solar radiation, UV and
thermal, is a process that affects polymeric
properties to some extent but at a slower rate. It is
reported that there is a synergistic effect between
photo oxidation and the biodegradation of
polyethylene. Treatments such as UV, thermal and
chemical leading to oxidation of the polymer surface
can be effectively used as a pretreatment strategy
before subjecting it to biodegradation. These
pretreatments lead to oxidation of the polymer
surface that decreases the hydrophobicity and
helps in the attachment of microorganism. The
attachment of organism to the polymeric surface
further enhances the biofilms formation. Microbes
utilize the functional groups like carbonyl, carboxyl
and ester produced on the polymer surface during
oxidation. Such studies are done with polyethylene
and have shown positive results in the form of
increase in the biodegradation with increase in the
irradiation time of UV.
Ambika Arkatkarand Mukesh DobleDepartment of Biotechnology,
Indian Institute of Technology Madras, Chennai-600036, India
Email : [email protected]
3
Environmental Degradation of Polyolefin's
I
ENVIS CENTRE Newsletter Vol.6, No.2 June 2008
SCIENTIFIC ARTICLES
Blends
Natural polymers like Poly lactic acid (PLA), Poly
å- caprolactone (PCL) and Polysaccharides can be
blended to some extent with the synthetic polymer. In
these blends the natural polymer being biodegradable
will help in the formation of biofilm on the surface.
Current research in our laboratory
We are studying the effect of various physical and
chemical pretreatment on the biodegradation of LDPE,
HDPE, starch blended PE and PP. Soil and marine
microorganisms have been isolated and are being
tested for their efficacy in carrying out the
biodegradation of these polymers. Several different
pretreatment strategies such as UV, thermal, chemical
are being tested to enhance the process. The
pretreated PP is then exposed to mixed soil culture.
The mixed soil culture is a suspension of soil sample
from a local dumping site. The experiments are carried
out in a minimal media. From our one year experiments
with thermally pretreated PP and mixed soil culture we
found good results. As already reported pretreatment
of the polymer surface works in synergy with microbial
attachment to enhance biodegradation. After one year
microorganism isolated from the mixed culture are
found to be Bacillus and Pseudomonas sp.
The polymer samples are monitored by
techniques like Baclight staining, Fourier transform
infrared (FTIR) spectroscopy, Differential scanning
calorimetry (DSC), Scanning electron microscopy
(SEM), Contact angle and Tensile strength etc.
Baclight staining helps us to observe live and dead
microorganisms on the polymer surface. SEM and
Contact angle measurements helps in studying
surface changes on the polymer whereas FTIR and
DSC techniques analyse the chemical and structural
changes in the polymer.
Further reading:
Arutchelvi, J., Sudhakar, M., Ambika Arkatkar,
Mukesh Doble, Sumit Bhaduri and Parasu Veera
Uppara (2008). Biodegradation of polyethylene
and polypropylene. Indian Journal of
Biotechnology. 7, 9-22.
Artham, T and Mukesh Doble. (2007).
Biodegradation of Aliphatic and Aromatic
Polycarbonates. Macromolecular Bioscience. doi
10.1002/mabi.200700106 (Press).
Sudhakar, M., Mukesh Doble, Sriyutha Murthy, P.,
and Venkatesan, R. (2007). Marine Microbe
Mediated Biodegradation of Low and High
D e n s i t y P o l y e t h y l e n e . I n t e r n a t i o n a l
B iodegardat ion and B iodeter io ra t ion .
doi:10.1016/j.ibiod.2007.07.011 (in press).
Sudhakar, M., Trishul, A., Mukesh Doble, Suresh
Kumar, K., Syed Jahan, S., Inbakandan,
Viduthalai, R., Umadevi, P., Sriyutha Murthy, P.
and Venkatesan, R. (2007). Biofouling and
biodegradation of polyolefins in ocean waters.
Polymer Degradation and Stability. 92,
1743-1752.
Sudhakar, M., Priyadarshini, Mukesh Doble,
Sriyutha Murthy, P., and Venkatesan, R. (2007).
Marine Bacteria Mediated Degradation of nylon
66 and 6. International Biodeterioration and
Biodegradation. 60, 144-151.
For more details contact :
Dr. Mukesh Doble, Ph. D.Lab : Bioengineering & Drug DesignProfessor, Department of BiotechnologyIIT Madras, Chennai - 600036, INDIA(Tel:044-2257 4107; Fax:044-2257 4102)Email : [email protected], [email protected] Website: http://www.biotech.iitm.ac.in/faculty/md.htm
ENVIS CENTRE Newsletter Vol.6, No.2 June 2008
The SEM analysis of the PP surface after 12 months
The Baclight staining of PP surface after 12 months (Live organism- green anddead organism- red in colour)
4
ndia is one of the main producer and
consumer of synthetic organic chemicals including
synthetic dyes. Synthetic dyes are used extensively in
textile dyeing, paper printing and colour photography
and also as additives in petroleum products. A wide
variety of synthetic dyes namely azo, polymeric,
anthraquinone, triphenylmethane and heterocyclic
dyes is used in textile dyeing processes. Worldwide
more than 10,000 dyes and pigments are used in
dyeing and printing industries. The total world
colourant production is estimated to be 8,00,000
tonnes per year and at least 10% of the used dyestuff
enters the environment through wastes (Levin et al.,
2004; Palmieri et al., 2005). The textile industry
accounts for two-thirds of the total dyestuff market (Riu
et al., 1998) and consumes large volumes of water and
chemicals for wet processing of textiles. An estimated,
10-15% of dye is discharged or lost into the effluents
during different dyeing processes (Zollinger, 2002).
Wastewaters from textile industries are a
complex mixture of many polluting substances like
acids, salts, organochlorine-based pesticides, heavy
metals, pigments, dyes etc., Due to complex nature
and hard-to-treat by conventional methods, textile
dyeing industries are facing problems to safe discharge
of wastewater. There have been several successful
methods developed based on physical and chemical
processes for colour removal of textile dyeing effluents.
They include coagulation/flocculation, membrane
fi l tration and activated carbon adsorption.
Unfortunately, these methods of effluent treatment
have high operating costs and limited applicability.
Further, these treatment methods produce large
quantities of sludge, which again create a problem in
waste disposal (Moreira et al., 2000). In recent years,
b io log ica l decolour izat ion us ing potent ia l
microorganisms capable of decolourizing and
detoxifying the synthetic dyes has been considered as
a p r o m i s i n g a n d e c o - f r i e n d l y m e t h o d
(Couto et al., 2005; Camarero et al., 2005).
Over the past few decades, numerous
microorganisms have been isolated and
characterized for decolourization of various groups
of synthetic dyes. In general, azo dyes are resistant
to bacterial degradation. However, certain bacteria
can degrade dyestuff by azoreductase activity
(Chung and Stevens, 1993). White rot fungi (WRF),
a group of basidiomycetous are the potential
organisms capable of mineralizing the complex
wood polymer and a wide variety of recalcitrant
compounds like xenobiotics, lignin and dyestuff by
their extracellular lignolytic enzyme system. WRF
offer significant advantages over bacterial system
since their extracellular lignolytic enzyme system
consisting of lignin peroxidases, manganese
dependent peroxidases, manganese independent
versatile peroxidases, and laccases and they
degrade a wide variety of complex aromatic
dyestuffs (Boer et al., 2004; Kamistsuji et al., 2005).
White-rot fungi do not require preconditioning to
particular pollutants, because enzyme secretion
depends on nutrient limitation, nitrogen or carbon,
rather than presence of pollutant. The extracellular
enzyme system also enables white-rot fungus
(WRF) to tolerate high concentration of pollutants
(Knapp et al., 1997).
However, the fungi in waste treatment and
bioremediation do not always enable the culture
conditions for lignolytic to be fulfilled. Other white rot
fungi namely Bjerkandera adusta, Irpex lacteus,
Plebioa radiata, Pleurotus ostreatus, P.sajor-caju,
Ganodema lucidum, Pycnoporus cinnabarinus and
Trametes versicolor have been demonstrated for the
decomposition of several recalcitrant dyes (Novotny
et al., 2001; Murugesan et al., 2006; 2007). The
enzymatic treatment of industrial waste has
exhibited several advantages over other physical
methods because it can be applied even to
compounds, which are biorefractory and it can be
operated at varied temperatures, pH and salinities.
Moreover, the enzymatic treatment of
wastes does not leave much sludge at the treatment
site. Much attention has been focused on the
development of processes to treat the wastewaters,
solid wastes, hazardous wastes and ameliorate
contaminated soils realizing the potential application
of enzyme treatments.
5ENVIS CENTRE Newsletter Vol.6, No.2 June 2008
Decolourization of Effluent using Immobilized Fungus
(Pleurotus sp. MAK-II)
M. Arulmani, K. Murugesan, V. Geetha andP.T. Kalaichelvan
Centre for Advanced Studies in BotanyUniversity of Madras, Guindy CampusChennai - 600 025, Tamil Nadu, India
Email : [email protected]
I
Agar Plate culture After 1 day
Immobilization of enzymes
Biodegradation appears to be a promising
technology, particularly the use of oxidative enzymes
as biocatalyst included with a microorganism or free
enzyme. Laccase has received particular attention
because of its ability to catalyze the oxidation of a wide
spectrum of molecules containing an aromatic ring
substituted with electron withdrawing groups
(D’Annibale et al., 1999). Enzyme immobilization
usually allows a good preservation of enzyme activity
over a long period (D’Annibale et al., 1999). The
efficiency of enzyme extract is enhanced by selective
adsorption when immobilized, as reported by Tatsumi
et al. (1996), in the removal of chlorophenols from
wastewaters by peroxidase immobilized on magnetite.
In most cases, laccases are immobilized on porous
beads. Xenobiotics are degraded in bed-packed
column reactors. However, immobilization of enzymes
on a membrane and the use of filtration offer several
advantages. First it allows the simultaneous
downstream separation of the transformation
products, when they are insoluble and secondly flow
rates can be higher than with packed beads, because
all the substrate flows through the support instead of
diffusing in the bead pores. Some of the intended
applications e.g. kraft pulp bleaching, dye effluent
using laccase involve high pH. Among the 40-50
known fungal laccases, a few are active at alkaline pH
(Schneider et al., 1999). Being added to alkaline
detergents, the laccases are able to oxidize various
textile dyes to bleach the undesirable colour in
washing solution.
Effluent treatment by immobilized mycelium
The efficiency of immobilized Pleurotus sp.
MAK-II for the decolourizing of the textile dye effluent
was assessed. Figure 1 shows the steps involved for
the textile dyeing effluent treatment with immobilized
mycelium of Pleurotus sp. MAK-II. The SEM
micrograph of immobilized fungus alginate beads was
completely different from that of the beads without
fungus. Table 1 shows the physicochemical properties
of the untreated and immobilized fungal treated
effluents. The initial and final pH of untreated effluent
was 9.5-9.8, whereas, the treated effluent pH after 15
days decreased to 7.0-7.2. The values of BOD and
COD found high in the untreated effluent, whereas the
immobilized mycelium of the test fungus removed up
to 75% and 80% of BOD and COD, respectively.
6ENVIS CENTRE Newsletter Vol.6, No.2 June 2008
Liquid plate culture After 5 days
Immobilization After 10 days
Growth of Immobilized culture at 120 rpm 2days.
After 15 daysNote the decolourization of
effluent at different days of treatment in Bioreactor.
Bioreactor
SEM of sodium alginate beads
Without cell Immobilization
With cellImmobilization
Fig. 1 Effluent treatment with immobilized mycelium of Pleurotus sp. MAK-II
Fig. 2 laccase activity by immobilized mucelium
of Pleurotus sp. MAK - II
Declolourization of the dye effluent and
De
colo
uriza
tion
(%
)
La
cca
se a
ctiv
ity (
U/m
L)
Incubation time (day)
th The fungus removed 55% of the colour on 15 day and
the maximum laccase activity of 27.81 U/mL observed thon 12 day (Fig. 2). Reduction of peak height in the UV
spectrum clearly indicate decolourization of effluent
(Fig. 3).
Fig. 3 UV-visible spectram of decolourization of effluent
by immobilized myceliam. Spectra after (1)1 day
(2) 5 days (3) 10 days (4) 15 days treatment.
Table 1. Physico-chemical propert ies of
untreated and treated effluents.
References
Levin, L., Papinutti, L. and Forchiassin, F. (2004).
Evaluation of Argentinean White Rot Fungi for
their ability to produce lignin-modifying enzymes
and decolourize industrial dyes. Bioresour.
Technol. 94, 169-176.
Palmieri, G., Cennamo, G. and Sannia, G. (2005).
Remazol brilliant blue R decolourisation by the
fungus Pleurotus ostreatus and its oxidative
enzymatic system. Enzyme Microb. Technol. 36,
17-24.
Riu, J., Schonsee, I. and Barcelo, D. (1998).
Determination of sulfonated azo dyes in
groundwater and industrial effluents by
automated solid-phase extraction followed by
capillary electrophoresis/ mass spectrometry. J.
Mass Spectro 33, 653-63.
Zollinger, H. (2002). Synthesis, properties and
applications of organic dyes and pigments.
Colour chemistry. New York: John Wiley-VCH
Publishers. Pp. 92-100.
Moreira, M.T., Mielgo, I., Feijoo, G. and Lema, J.M.
(2000). Evaluation of different fungal strains in
the decolourization of synthetic dyes. Biotechnol.
Lett. 22, 1499-1503.
Couto, S.R., Sanroman, M.A. and Gubitz, G.M.
(2005). Influence of redox mediators and metal
ions on synthetic acid dye decolorization by
crude laccase from Trametes hirsuta.
Chemosphere 58, 417-22.
Camarero, S., Ibarra, D., Martinez, M.A. and
Martinez, A.T. (2005). Lignin-derived compounds
as efficient laccase mediators for decolourization
of different types of recalcitrant dyes. Appl.
Environ. Microbiol. 71, 1775-1784.
Chung, K.T. and Stevens, S.J. (1993).
Decolourization of azo dyes by environmental
microorganism and helminthes. Environ. Toxicol.
Chem. 12, 2121-2132.
7ENVIS CENTRE Newsletter Vol.6, No.2 June 2008
Colour
Odour
pH
BOD (mg/L)
COD (mg/L)
Dark blue
Offensive
9.5 - 9.8
4500
14000
Light blue
No odour
7.0 - 7.2
1120
2800
Untreated Treated
ParameterEffluent and Medium (1:1)
Ab
sorb
an
ce
Wavelength (nm)
Boer, C.G., Obici, L., De’Souza, C.G.M. and Piralta,
R.M. (2004). Decolourization of synthetic dyes by
solid state culture of Lentinula (Lentinus) edodes
producing manganese peroxidase as the main
lignolytic enzyme. Bioresour. Technol. 94, 107-
112.
Kamitsuji, H.Y., Watanabe, T. and Kuwhara, M. (2005). 2+Mn is dispensable for the production of active
MnP2 by Pleurotus ostreatus. Biochem. Biophy.
Res. Commun. 327, 871-876.
Knapp, J.S., Zhang, F. and Tpley, N.K. (1997).
Decolourization of oranges 11 by a Wood-Rooting
Fungus. J. Chemical. Technol. Biotech. 69, 289-
296.
Novotny, C., Rawal, B., Bhatt, M., Patel, M., Sasek, V.
and Molotoris, H.P. (2001). Capacity of Irpex
l ac teus and P leu ro tus os t r ea tus f o r
decolourization of chemically different dyes. J.
Biotechnol. 89, 113-122.
Murugesan, K., Arulmani, M., Nam, I.H., Kim, Y.M.,
Chang, Y.S. and Kalaichelvan, P.T. (2006).
Purification and characterization of laccase
produced by a White Rot Fungus Pleurotus sajor-
caju under submerged culture condition and its
potential in decolourization of azo dyes. Appl.
Microbiol. Biotechnol. 72, 939-946.
Murugesan, K., Nam, I.H., Kim, Y.M. and Chang, Y.S.
(2007). Decolorization of reactive dyes by a
thermostable laccase produced by Ganoderma
lucidum in solid state culture. Enzyme Microb.
Technol. 40, 1662-1672.
D’Annibale, A., Stasi, S.R., Vnciguerra, V., Di-Mattia,
E. and Sermanni, G.G. (1999). Characterization of
immobilized laccase from Lentinula edodes and its
use in olive-mill waste water treatment. Process
Biochem. 34, 697-704.
Tatsumi, K., Wada, S. and Ichikawa, H. (1996).
Removal of chlorophenols from wastewater by
immobilized horseradish peroxidase. Biotechnol.
Bioeng. 51, 126-130.
Schneider, P., Caspersen, M.B., Mondorf, K., Halkier,
T., Skov, L.K., Ostergarrd, R.R., Brown, K.M.,
Brown, S.H. and Xu, F. (1999). Characterization of
a Coprinus cinereus laccase. Enzyme Microb.
Technol. 25, 502-508.
oil salinity is a major problem that makes
soil unfit for Agriculture. Historical records of the
past 6000 years of civilization evidenced that,
humans have never been able to continue a
progressive civilization in one locality for more than
200 to 800 years. The major reason for the decline of
any civilization in any area seems to have been the
destruction of the resources base of that area. In
Mesopotamia, major salinity damage occurred from
2400 BC to 1700 BC and the slow increase in salinity
caused a decline in agriculture productivity to as
approximately as 65% over a 700-year period.
At present salinity is one of the most serious
environmental problems influencing crop growth
around the world. In India, 7 m ha are affected by
salinity and alkalinity and marginal decrease of
productivity is expected from these lands. In
Tamilnadu coast, salt causes stress and damage on
the plant during the vegetation period from
germination – emergence through growth –
development and harvesting time.
It is generally accepted that three major
hazards are associated with saline habitats. These
may be described as follows:
(a) Water stress arising from the more negative
water potential (elevated osmotic pressure) of
the rooting medium.
(b) Specific with toxicity usually associated with
either excessive chloride or sodium intake , and
(c) Nutrient ion imbalance when the excess of
sodium or chloride leads to a diminished uptake
of potassium, nitrate, or phosphate or due to
impaired internal distribution of one or another
of these ions.
8ENVIS CENTRE Newsletter Vol.6, No.2 June 2008
Prospects of Marine Biofertilizers for Saline Soil Crop Cultivation
S. RavikumarDepartment of Oceanography and Coastal Area StudiesAlagappa University, Thondi Campus, Thondi – 623 409,
Ramanathapuram District , Tamilnadu, India.Email : [email protected]
S
living organisms in the soil and are associated with
mangrove and associated plant species.
Azospirillum are plumpy, slightly curved and straight
rods gram negative to gram variable. They are motile
in liquid media by a single plar flagellum.
Four species of Azospirillum such as
Azospirillum lipoferum, A.brasilense, A.halopreferns
and A.irakense were identified from the marine
sediments. Of them, Azospirillum lipoferum was
found to be the dominant species. All these species
were found to have tolerance ability to various -1 -1salinity levels (0- 35 g.1 ) and grown better in 30g. 1
NaC1. However, the level of phytohormone
Production (IAA) and the rate of nitrogen fixation was -1better at 10 g .1 NaC1 and reduced activity could be
observed at higher salinity levels. Moreover all these
species could be used as marine biofertilizers. Of
them, Azospirillum brasilense are preferable than the
other species.
Group Phosphate Solubilising Bacteria (PSB)
Phosphorous is an important limiting
nutrients. The phosphate form of phosphorous is one
of the least soluble mineral nutrients in soil. The -1phosphorous content of soils may range up to 19 g k
but usually less that 5 % of this is available to the
plants and microorganisms in soluble form and the
rest 95 % is unavailable being in the form of insoluble
inorganic phosphate and organic phosphorous
complexes. These forms of phosphorous being held
in the sediments far a long time remain excluded from
cycling. Microbes play a significant role in the
transformation of phosphorous and referred to as
phosphobacteria. Eight species of saline tolerant
inorganic phosphate solubilizing bacteria such as
Bacillus subtil is, B.cereus, B.megaterium,
Arthrobacter illicis, Escherichia coli, Pseudomonas
aeruginosa, Enterobacter aerogenes and
Micrococcus luteus were identified. Of them, Bacillus
subtilis was predominantly found in mangrove
sediments.
All the nine species could able to grow better -1 at 4 g.1 NaCl concentrations. However the
-1 phosphatase activity was good at 2 g1 NaCl salinity
levels. Moreover except Pseudomonas aeruginosa
9ENVIS CENTRE Newsletter Vol.6, No.2 June 2008
More than that, inoculation of crops with any useful
microorganisms would not yield desired success.
Excess salts in soil adversely affect the survival, growth
and nutrient supply to the plants.
thDuring late 20 century, research has been
started to find out the saline tolerant Azotobacter and
Phosphobacteria from marine aquatic sediments but
focus on the preparation of marine biofertilizer for
coastal agriculture has not been made. Recently,
identification of saline tolerant biofertilizers for possible
utility to use for agricultural crop cultivation has been
recognized. Besides that microbial biofertilizers have
also been identified to improve the growth of mangrove
plants. Azotobacter, Azospirillum, Phosphobacter and
Phosphate producing bacteria and Blue Green algae
were isolated and identified from saline sediments.
Even the presence of high phenolic compounds and
prevalent anaerobic condition in the mangrove habitat
and their biofertilizer effects have been proved with the
rice and balckgram crop seedlings. Compared with the
existing biofertilizers the morphological and
biochemical characteristics are similar except the
saline induced effects on growth and physiology.
Genus Azotobacter
Azotobacters are aerobic, free-living,
thermotrophic bacteria with unique ability of fixing
atmospheric nitrogen. The bacteria are gram negative,
often motile by peritrichous flagella or non-motile. The
Azotobacters produce copious amount of capsular
slime. They do not or endospores but some species
may form cysts. Three species of Azotobacters such as
Azotobacter chroococcum, A.berijerinkii and A.
vivelandii were identified from mangrove rhizosphere
sediments. All the three species are able to tolerate -1high saline concentrations (up to 35 g 1 and 30 g 1 ).
These species of Azotobacter enhanced the
germination and growth of rice and black gram
seedling even at high saline conditions by fixing
atmospheric nitrogen and producing phytohormones.
Among them, A.chroococcum was h igh ly
recommended than the other bacterial species.
Genus Azospirillum
Azospirillum species are free living bacteria
know to fix atmospheric nitrogen. They occur as free
-1
and Micrococcus luteus, all the other species of
bacteria could be used as a biofertilizer to enhance the
growth of rice seedlings. Of them Bacillus Megaterium
could be used as a marine biofertilizer for saline soil
cultivation.
Group Phosphatase Producing Bacteria (PPB)
Organic phosphorous in the marine
environment is macromolecular and not readily
available for incorporation into the marine organisms.
So the organic phosphorous compounds are to be pre-
conditioned by extra cellular bacterial enzymes called
“phosphatases” for making them available to the
nutrient cycles. Three groups of bacteria viz.,
Pseudomonas, Vibrio and Bacillus were identified from
mangrove sediments. Of them, Bacillus cereus was
dominant form and the phosphatase activity was also
higher. All the three groups of PPB could enhance the -1 growth of rice seedlings at 25 g. 1 NaCl level of soil
salinity at which the phosphatase activity was
significantly high.
Recommended biofertilizers for the saline soil
crop cultivation on priority basis.
10ENVIS CENTRE Newsletter Vol.6, No.2 June 2008
Biofertilizer
Azospirillum
Azotobacter
Inorganic phosphate
solubilizing bacteria
Phosphatase producing
bacteria
Black gram, Rice
Black gram, Rice
Black gram, Rice
Rice
Recommended crop species
Species abundance of sal ine tolerant biofertilizers in the mangrove sediments
Phosphate solubilizing bacteria
Azospirillum
Phosphate producing bacteria
Azotobacter
RESEARCH REPORTS
ceanic lithosphere exposed at the sea
floor undergoes seawater–rock alteration reactions
involving the oxidation and hydration of glassy
basalt. Basalt alteration reactions are theoretically
capable of supplying sufficient energy for
chemolithoautotrophic growth . Such reactions
have been shown to generate microbial biomass in
the laboratory, but field-based support for the
existence of microbes that are supported by basalt
alteration is lacking. Here, using quantitative
polymerase chain reaction, in situ hybridization and
microscopy, we demonstrate that prokaryotic cell
abundances on seafloor-exposed basalts are 3–4
orders of magnitude greater than in overlying deep
sea water. Phylogenetic analyses of basaltic lavas
from the East Pacific Rise (9° N) and around Hawaii
reveal that the basalt-hosted biosphere harbours
high bacterial community richness and that
community membership is shared between these
sites. We hypothesize that alteration reactions fuel
chemolithoautotrophic microorganisms, which
constitute a trophic base of the basalt habitat, with
important implications for deep-sea carbon cycling
and chemical exchange between basalt and sea
1
Cara M. Santelli, Beth N. Orcutt, Erin Banning,
Wolfgang Bach, Craig L. Moyer, Mitchell L. Sogin,
Hubert Staudigel & Katrina J. Edwards
Geomicrobiology Group, Department of Biological
Sciences, Marine Environmental Biology, University
of Southern California, 3616 Trousdale Boulevard,
Los Angeles, California 90089-0371,USA.
Abundance and diversity of microbial life
in ocean crust. Nature 453, 2008, 653-656 .
Abundance and Diversity of Microbial life in Ocean Crust
O
11ENVIS CENTRE Newsletter Vol.6, No.2 June 2008
ONLINE REPORTS ON MICROORGANISMS
Seafloor Diversity Points to Origin of Life
cientists now have found "thousands of times of more bacteria on the seafloor than in the water above," according to a statement. The findings were made at two sites, suggesting that rich microbial life extends across the ocean floor, says University of Southern California geomicrobiologist Katrina J. Edwards.
These results, along with a separate discovery announced very recently existence of life a mile below the seafloor, have made the scientists to wonder if life on Earth began along shorelines or perhaps originated in the planet's marine belly.
Surprising diversity
Using genetic analysis, Edwards and colleagues found higher microbial diversity on common, basalt rocks compared with other marine locations, such as those found at hydrothermal vents. The diversity on the seafloor rocks was as rich as that in common farm soil.
"We now know that there are many more such microbes than anyone had guessed," said David L. Garrison, Director of the National Science Foundation’s biological oceanography program. The findings are detailed in the May 29 issue of the journal Nature.
The big question now is where from all these newfound bacteria get the energy they need to survive."We scratched our heads about what was supporting this high level of growth when the organic carbon content is pretty darn low," Edwards said. Perhaps, the researchers figured, chemical reactions with the rocks themselves might offer fuel for life. Lab tests also confirmed the idea.
Evolving ideas
The research supports the idea that some bacteria survive on energy from the crust, a process that could affect knowledge about the deep-sea carbon cycle and even the evolution of early life.
For example, many scientists think shallow
water, not deep water, cradled the planet’s first life.
They reason that the dark carbon-poor depths appear
to offer little energy, and rich environments like
hydrothermal vents are relatively sparse. But the
newfound abundance of seafloor microbes makes it
theoretically possible that early life thrived—and
may be even began—on the seafloor.
"Some might even favor the deep ocean for
the emergence of life since it was a bastion of
stability compared with the surface, which was
constantly being blasted by comets and other
objects," Edwards says.
Much more research needs to be done,
however. Edwards and more than 30 colleagues
plan to take a microbial lab to the seafloor 15,000
feet (4.5 kilometers) below the surface, to study the
bacteria further. They'll drill down through 109 yards
(100 meters) of sediments and 547 yards (500
meters) of bedrock to study how the bacteria alter
rock and to measure biodiversity below the seafloor.
This work should shed light on whether the
bacteria evolved from ancestors that floated down
from above or from some as yet unknown source
deep in the crust.
The research was funded by the NSF,
NASA Astrobiology Institute and Western
Washington University.
(Source: Livescience.com, 2008)
S
Microbes Mutated in Outer Space become far More Dangerous
almonella bacteria sent into outer space
responded to the altered gravity by becoming more
virulent, with changed expression of 167 different
genes, according to a study published in the
Proceedings of the National Academy of Sciences.
"These bugs can sense where they are by
changes in their environment," said Cheryl
Nickerson, from the Center for Infectious Diseases
and Vaccinology at Arizona State University (ASU).
"The minute they sense a different environment,
they change their genetic machinery so they can
survive.“
Researchers placed strains of Salmonella
typhimurium, a common food-poisoning agent, into
two separate containment canisters. One of the
canisters was sent into outer space for 12 days,
S
12
while the other remained in the Orbital Environmental
Simulator at Kennedy Space Center. The
environmental simulator remained in constant
communication with the space shuttle, immediately
replicating in real-time whatever temperature and
humidity conditions were being experienced in the
vessel. This allowed the two groups of bacteria to be
exposed to identical conditions, except for the fact that
one group were under microgravity conditions in outer
space.
The findings may be significant not only for
those who travel in space, but also in terms of what
microbes astronauts are bringing back.
"Wherever humans go, microbes go; you can't
sterilize humans," Nickerson says. "Wherever we go,
under the oceans or orbiting the Earth, the microbes go
with us, and it's important that we understand how
they're going to change.“
Nickerson also says that since S. typhimurium
exists in a natural microgravity in the human gut,
understanding how environmental conditions regulate
the organism's virulence may help lead to better
treatments.
In addition to researchers from ASU, scientists
also participated in the study from the Johnson and
Kennedy Space Centers, Kimmel Cancer Center,
NASA Ames Research Center, Oklahoma City
University, Tulane University, University of Arizona,
University of Chicago, University of Colorado at
Boulder and Denver, Southeast Louisiana Veterans
Health Care System, and the Max Planck Institute for
Infection Biology in Berlin.
(Source: naturalnews.com, 2008)
Microbes as Climate Engineers
e might think that we could control the
climate but unless we harness the powers of our
microbial co-habitants on this planet we might be
fighting a losing battle, according to an article in the
February 2008 issue of Microbiology Today.
Humans are continually altering the
atmosphere. “Arrogant organisms that we are, it is
easy to view this as something entirely novel in
Earth’s history,” says Dr Dave Reay from the
University of Edinburgh. “In truth of course, micro-
organisms have been at it for billions of years.”
Humans affect the atmosphere indirectly by
their activities. Most human-induced methane
comes from livestock, rice fields and landfill: in all of
these places, microbes are actually responsible for
producing the methane, 150 million tonnes a year.
Microbes in wetlands produce an additional 100
million tonnes and those that live inside termites
release 20 million tonnes of methane annually.
About 90 billion tonnes of carbon a year is
absorbed from the atmosphere by the oceans, and
almost as much is released; microbes play a key
role in both. On land, a combination of primary
p roduc t i on , r esp i r a t i on and m i c rob i a l
decomposition leads to the uptake of 120 billion
tonnes of carbon every year and the release of 119
billion tonnes.
“The impact of these microbially-controlled
cycles on future climate warming is potentially
huge,” says Dr Reay. By better understanding these
processes we could take more carbon out of the
atmosphere using microbes on land and in the sea.
Methane-eating bacteria can be used to catch
methane that is released from landfi l l ,
Cyanobacteria could provide hydrogen fuel, and
plankton have already become a feedstock for
some biofuels.
“Microbes will continue as climate
engineers long after humans have burned that final
barrel of oil. Whether they help us to avoid
dangerous climate change in the 21st century or
push us even faster towards it depends on just how
well we understand them.
(Source: sciencedaily.com, 2008).
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ENVIS CENTRE Newsletter Vol.6, No.2 June 2008
13
icrobes could provide a clean, renewable
energy source and use up carbon dioxide in the
process, suggests Dr James Chong at a Science
Media Centre press briefing. Methanogens are
microbes called archaea that are similar to bacteria.
They are responsible for the vast majority of methane
produced on earth by living things says Dr Chong from
York University. They use carbon dioxide to make
methane, the major flammable component of natural
gas. So methanogens could be used to make a
renewable, carbon neutral gas substitute.
Methanogens produce about one billion tones
of methane every year. They thrive in oxygen-free
environments like the guts of cows and sheep, humans
and even termites. They live in swamps, bogs and
lakes. Increased human activity causes methane
emissions to rise because methanogens grow well in
rice paddies, sewage processing plants and landfill
sites, which are all made by humans.
Methanogens could feed on waste from farms,
food and even our homes to make biogas. This is done
in Europe, but very little in the UK. The government is
now looking at microbes as a source of fuel and as a
way to tackle food waste in particular.
Methane is a greenhouse gas that is 23 times
more effective at trapping heat than carbon dioxide. By
using methane produced by bacteria as a fuel source,
we can reduce the amount released into the
atmosphere and use up some carbon dioxide in the
process.
(Source: sciencedaily.com, 2007)
than was suspected. Before a cloud can produce
rain or snow, rain drops or ice particles must form.
Act as nuclei
This requires the presence of aerosols: tiny
particles that serve as the nuclei for condensation.
Most such particles are of mineral origin, but
airborne microbes – bacteria, fungi or tiny algae –
can do the job just as well. Unlike mineral aerosols,
living organisms can catalyze ice formation even at
temperatures close to 0 degrees Celsius.
Now a team, led by Brent Christner, a
microbiologist at Louisiana State University in Baton
Rouge, has managed to catalogue these rain-
making microbes by looking at fresh snow collected
at various mid-and high-latitude locations in North
America, Europe and Antarctica. They filtered the
snow sample to remove particles, put those
particles into containers of pure water, and slowly
lowered the temperature, watching closely to see
when the water froze.
The higher the freezing temperature of any
given sample, the greater the number of nuclei and
the more likely they are to be biological in nature. To
tease apart these two effects, the team treated the
water samples with heat or chemicals to kill any
bacteria inside, and again checked the freezing
temperatures of the samples.
Mostly biological
In this way they found between 4 and 120
ice nucleators per litre of melted snow. Some 69 per
cent to 100 percent of these particles were probably
biological. The results were published in the journal
Science. The researchers were surprised to find
‘rain-making’ bacteria in all samples; the snow from
Antarctica had fewer than that from France and
Montana, but it still had some.
“Biological particles do seem to play a very
important part in generating snowfall and rain,
especially at relatively warm cloud temperatures,”
says Christner. Some scientists note that this
freezing ability also means that the bacteria get out
of clouds and back to Earth more quickly.
Methane from Microbesa Fuel for the Future
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ENVIS CENTRE Newsletter Vol.6, No.2 June 2008
Rain- Making Bacteria found Worldwide
NEWS
T he same bacteria that cause frost damage on
plants can help clouds to produce rain and
snow. Studies on freshly fallen snow suggest that
‘bio-precipitation’ might be much more common
14
Human factor
Changes in land-use, forestry and agriculture,
such as expanding monoculture, change the
composition of microbes in the atmosphere. As
biological components seem to have a large role in
how rain forms, such changes may affect rainfall and
climate in many places on Earth. “It is about time for
atmospheric and climate scientists to start thinking
about the implications,” says Christner.
(Source: ”The Hindu” Dated: 15 May, 2008)
ne week summer workshop on “Fungal
biotechnology” was jointly organized by Dr. V.
Kaviyarasan and Prof. J. Muthumary, Centre for
Advanced Studies in Botany, University of Madras,
Guindy Campus, Chennai – 600 025 from May 24,
2008 to June 01, 2008.
The programme was structured with basic
techniques such as isolation, identification,
preservation, gene transfer technology, DNA isolation
and RAPD, Mycorrhizal biotechnology, IPR and
Biosafety for the benefit of the participants. Eminent
researchers Profs. Vittal, Rengasamy, Muthumary,
Mathivanan, Kaviyarasan and Palani from Centre for
Advanced Studies in Botany, University of Madras and
Dr. Perumal from Murugappa Chettiar Research
Centre and Dr. Mohan, Institute of Forest Genetics and
Tree Breeding delivered lecturers and gave laboratory
demonstrations on various aspects related to fungal
biotechnology. Many teachers, Ph.D researchers from
various colleges and Universities participated in the
workshop and learned various techniques on fungal
biotechnology.
Summer Workshop on Fungal Biotechnology
MEETING REPORT
Dr. V. KaviyarasanCentre for Advanced Studies in Botany, University of Madras, Guindy Campus, Chennai – 600 025E-mail: [email protected]
Abstracts of Recent Publications
001 - Asha Rani , Shalini Porwal , Rakesh Sharma ,
Atya Kapley , Hemant, Purohit ,Vipin Chandra Kalia.
Institute of Genomics and Integrative Biology
(IGIB), CSIR, Delhi University Campus, Mall Road,
Delhi – 110007, India. Assessment of microbial
diversity in effluent treatment plants by culture
dependent and cu l ture independent
approaches. Bioresource Technology, 2008, 1 –
10.Microbial community structure of two
distinct effluent treatment plants (ETPs) of pesticide and pharmaceutical industries were assessed and defined by (i) culture dependent and culture independent approaches on the basis of 16S rRNA gene sequencing, and (ii)diversity index analysis – operational taxonomic units (OTUs). A total of 38 and 44 bacterial OTUs having 85–99% similarity with the closest match in the database were detected among pharmaceutical and pesticide sludge samples, respectively. Fifty percent of the OTUs were related to uncultured bacteria. These OTUs had a Shannon diversity index value of 2.09–2.33 for culturables and in the range of 3.25–3.38 for unculturables. The high species evenness values of 0.86 and 0.95 indicated the vastness of microbial diversity retrieved by these approaches. The dominant cultured bacteria indicative of microbial diversity in functional ETPs were Alcaligenes, Bacillus and Pseudomonas. Brevundimonas, Citrobacter, Pandoraea and Stenotrophomonas were specific to pesticide ETP, where as Agrobacterium, Brevibacterium, Micrococcus, Microbacterium, Paracoccus and Rhodococcus were specific to pharmaceutical ETP. These microbes can thus be maintained and exploited for efficient functioning and maintenance of ETPs.Keywords: Effluent; Metagenomics; Microbial diversity; Unculturable; 16S rRNA gene.
002- Lisa M. Gieg, Kathleen E. Duncan, and Joseph M. Suflita. Department of Botany and Microbiology, University of Oklahoma, 770 Van Vleet Oval, Rm. 135, Norman, OK 73019. Bioenergy Production via Microbial Conversion of Residual Oil to Natural Gas. Applied and Environmental Microbiology, 74, 2008, 3022-3029.
World requirements for fossil energy are expected to grow by more than 50% within the next
O
ENVIS CENTRE Newsletter Vol.6, No.2 June 2008
15
25 years, despite advances in alternative
technologies. Since conventional production methods retrieve only about one-third of the oil in
place, either largenew fields or innovative strategies for recovering energy resources from existing fields
are needed to meet the burgeoning demand. The
anaerobic biodegradation of n-alkanes to methane gas hasnow been documented in a few studies, and
it was speculated that this process might be useful for recovering energy from existing petroleum
reservoirs. We found that residual oil entrained in a
marginal sandstone reservoir core could be converted to methane, a key component of natural
gas, by an oil-degrading methanogenic consortium. Methane production required inoculation, and rates
ranged from 0.15 to 0.40 µmol/day/g core (or 11 to 31 µmol/day/g oil), with yields of up to 3 mmol CH /g 4
residual oil. Concomitant alterations in the hydrocarbon profile of the oil-bearing core revealed
that alkanes were preferentially metabolized. The consortium was found to produce comparable
amounts of methane in the absence or presence of sulfate as an alternate electron acceptor. Cloning
and sequencing exercises revealed that the inoculum comprised sulfate-reducing, syntrophic,
and fermentative bacteria acting in concert with aceticlastic and hydrogenotrophic methanogens.
Collectively, the cells generated methane from a variety of petroliferous rocks. Such microbe-based
methane production holds promise for producing a clean-burning and efficient form of energy from
underutilized hydrocarbon-bearingresources.
Keywords: Res idual Oi l , Natura l Gas,
biodegradation, alkanes, methane, Microbial
Conversion.
003 - R. Vílchez, C. Pozo, M. A. Gómez, B. Rodelas
and J. González-López. Helmholtz Center for Infection Research, Department of Cell Biology and
Immunology, Inhoffenstrabe 7, D-38124
Braunschweig, Germany. Dominance of
sphingomonads in a copper-exposed biofilm
community for groundwater treatment.
Microbiology, 153, 2007, 325-337.
The structure, biological activity and microbial biodiversity of a biofilm used for the
removal of copper from groundwater were studied and compared with those of a biofilm grown under
copper-free conditions. A laboratory-scale submerged fixed biofilter was fed with groundwater
–1 –1(2.3 l h ) artificiallypolluted with Cu(II) (15 mg l ) and –1amended with sucrose (150 mg l ) as carbon
source. Between 73 and 90 % of the Cu(II) was removed from water during long-term operation
(over 200 days). The biofilm was a complex ecosystem, consisting of eukaryotic and prokaryotic
micro-organisms. Scanning electron microscopy revealed marked structural changes in the biofilm
induced by Cu(II), compared to the biofilm grown in absence of the heavy metal. Analysis of cell-bound
extracellular polymeric substances (EPS) demonstrated a significant modification of the
composition of cell envelopes in response to Cu (II). Transmission electron microscopy and energy-
dispersive X-ray microanalysis (EDX) showed that copper bioaccumulated in the EPS matrix by
becoming bound to phosphates and/or silicates, w h e r e a s c o p p e r a c c u m u l a t e d o n l y
intracytoplasmically in cells of eukaryotic microbes. Cu(II) also decreased sucrose consumption, ATP
content and alkaline phosphatase activity of the biofilm. A detailed study of the bacterial community
composition was conducted by 16S rRNA-based temperature gradient gel electrophoresis (TGGE)
profiling, which showed spatial and temporal stabilityof the species diversity of copper-exposed biofilms
during biofilter operation. PCR reamplification and sequencing of 14 TGGE bands showed
the prevalence of alphaproteobacteria, with most sequences (78 %) affi l iated to the
Sphingomonadaceae. The major cultivable colony type in plate counts of the copper-exposed biofilm
was also identified as that of Sphingomonas sp. These data confirm a major role of these organisms
in the composition of the Cu (II)-removingcommunity.Keywords: Groundwater treatment, biological
activity, biofilm, eukaryotic microbes, rRNA, PCR,
alkaline.
004- Catherine A. Lozupone and Rob Knight.
Departments of Molecular, Cellular, and
Developmental Biology and Chemistry and
Biochemistry, University of Colorado, Boulder, CO
80309. Global patterns in bacterial diversity.
PNAS, 104, 2007, 11436-11440.
Microbes are di ff icul t to cul ture.
Consequently, the primary source of information
about a fundamental evolutionary topic, life’s
diversity, is the environmental distribution of gene
sequences. We report the most comprehensive
analysis of the environmental distribution of bacteria
to date, based on 21,752 16S rRNA sequences
ENVIS CENTRE Newsletter Vol.6, No.2 June 2008
16
compiled from 111 studies of diverse physical
environments. We clustered the samples based on
similarities in the phylogenetic lineages that they
contain and found that, surprisingly, the major
environmental determinant of microbial community
composition is salinity rather than extremes of
temperature, pH, or other physical and chemical
factors represented in our samples. We find that
sediments are more phylogenetically diverse than
any other environment type. Surprisingly, soil, which
has high species-level diversity, has below-average
phylogenetic diversity. This work provides a
framework for understanding the impact of
environmental factors on bacterial evolution and for
the direction of future sequencing efforts to discover
new lineagesKeywords: environmental distribution, microbial
ecology, phylogenetic diversity, UniFrac, bacterial
diversity.
005- Daisuke Inoue, Shoji Hara, Mari Kashihara,
Yusaku Murai, Erica Danzl, Kazunari Sei,Shinji
Tsunoi, Masanori Fujita, and Michihiko Ike. Division of
Sustainable Energy and Environmental Engineering,
Osaka Univers i ty, 2-1Yamadaoka, Sui ta,
Osaka 565-0871, Japan. Degradation of Bis(4-
Hydroxyphenyl)Methane (Bisphenol F) by
Sphingobium yanoikuyae Strain FM-2 Isolated
from River Water. Applied and Environmental
Microbiology, 74, 2008, 352–358.
Three bacteria capable of utilizing bis(4-hydroxyphenyl)methane (bisphenol F [BPF]) as the sole carbon source were isolated from river water, a n d t h e y a l l b e l o n g e d t o t h e f a m i l y Sphingomonadaceae. One of the isolates, designated Sphingobium yanoikuyae strain FM-2, at an initial cell density of 0.01 (optical density at 600 nm) completely degraded 0.5 mM BPF within 9 h without any lag period under inductive conditions. Degradation assays of various bisphenols revealed that the BPF-metabolizing system of strain FM-2 was effective only on the limited range of bisphenols consisting of two phenolic rings joined together through a bridging carbon without any methyl substitution on the rings or on the bridging structure. A BPF biodegradation pathway was proposed on the basis of metabolite production patterns and identification of the metabolites. The initial step of BPF biodegradation involves hydroxylation of the bridging carbon to form bis(4-hydroxyphenyl) methanol, fo l lowed by oxidat ion to 4,4-d i h y d r o x y b e n z o p h e n o n e . T h e 4 , 4 -dihydroxybenzophenone appears to be further
oxidized by the Baeyer-Villiger reaction to 4-hydroxyphenyl 4-hydroxybenzoate, which is then cleaved by oxidation to form 4-hydroxybenzoate and 1,4-hydroquinone. Both of the resultant simple aromatic compounds are mineralized.Keywords: Microbial Conversion, alkanes,
methane, Bioenergy Production, Residual Oil,
Natural Gas.
006- Kathryn A. Harrison, Roland Bol, Richard D.
Bardgett. Soil and Ecosystem Ecology Laboratory,
Institute of Environmental and Natural Sciences,
Lancaster University, Lancaster, LA1 4YQ, UK. Do
plant species with different growth strategies
vary in their ability to compete with soil
microbes for chemical forms of nitrogen? Soil
Biology & Biochemistry, 40, 2008, 228–237.
We used dual labelled stable isotope (13 C
and 15 ) techniques to examine how grassland N
plant species with different growth strategies vary
in their ability to compete with soil microbes for
different chemical forms of nitrogen (N), both
inorganic and organic. We also tested whether
some plant species might avoid competition by
preferentially using different chemical forms of N
than microbes. This was tested in a pot experiment
where monocultures of five co-existing grassland
species, namely the grasses Agrostis capillaris,
Anthoxanthum odoratum, Nardus stricta,
Deschampsia flexuosa and the herb Rumex
acetosella, were grown in field soil from an acid
semi-natural temperate grassland. Our data show
that grassland plant species with different growth
strategies are able to compete effectively with soil
microbes for most N forms presented to them,
including inorganic N and amino acids of varying
complexity. Contrary to what has been found in
strongly N limited ecosystems, we did not detect
any differential uptake of N on the basis of chemical
form, other than that shoot tissue of fast-growing
plant species was more enriched in 15 from N
ammonium-nitrate and glycine, than from more
complex amino acids. Shoot tissue of slow-
growing species was equally enriched in 15N from
all these N forms. However, all species tested,
least preferred the most complex amino acid
phenylalanine, which was preferentially used by
soil microbes. We also found that while fast-
growing plants took up more of the added N forms
than slow-growing species, this variation was not
related to differences in the ability of plants to
ENVIS CENTRE Newsletter Vol.6, No.2 June 2008
17
compete with microbes for N forms, as hypothesised.
On the contrary, we detected no difference in microbial
biomass or microbial uptake of 15N between fast and
slow-growing plant species, suggesting that plant
traits that regulate nutrient capture, as opposed to
plant species-specific interactions with soil microbes,
are the main factor controlling variation in uptake of N
by grassland plant species. Overall, our data provide
insights into the interactions between plants and soil
microbes that influence plant nitrogen use in
grassland ecosystems.Keywords: Amino acids; Grassland; Organic
nitrogen; Inorganic nitrogen; Microbial biomass; Plant-
microbial competition; Stable isotopes; Growth
strategies; Nitrogen.
NATIONAL
1. Tata Institute of Fundamental Research (TIFR), Mumbai. http://www.tifr.res.in
2. Tamilnadu Agricultural University (TNAU), Coimbatore. http://www.tnau.ac.in
3. Central Food Technological Research Institute (CFTRI), Mysore. http://www.cftri.com
4. Central Institute of Brackish water Aquaculture (CIBA), Chennai. http://www.ciba.res.in
5. Defence Food Research Laboratory (DFRL), Mysore. http://www.mylibnet.org/dfrl.html
6. National Facility for Marine Cynobacteria (NFMC), Thiruchirapalli. http://www.ncbs.res.in.
7. National Institute of Oceanography (NIO), Goa. http://www.nio.org
INTERNATIONAL
1. American Museum of Natural History http://www.amnh.org/nationalcenter/infection/
2. The site for cool pictures of microbes (or) This site with all animations and a complete video library is on the CELLS alive.
http://www.cellsalive.com/mitosis.htm
3. Digital Learning Centre for Microbial Ecology http://commtechlab.msu.edu/
4. An Action Bioscience
http://www.actionbioscience.org/
5. Environmental Literacy Council
http://www.enviroliteracy.org/article.php/532.html
6. United Nations Environment Programme. http://www.unep.org
7. Scottish Microbiology Society
http://www.scottish-microbiology.org.uk
- G l u t a t h i o n e a n d r e l a t e d t h i o l i n microorganisms and plants: August 27 - 29, 2008. Venue: Nancy, France. Website: https://matar.ciril.fr/THIOL/homephar.php.
- Evolving microbial food quality and safety (FOOD MICRO 2008): September 1 - 3, 2008. Venue: Aberdeen, Aberdeen Exhibition and Conference Centre (AECC), U.K. Website: http://www.foodmicro2008.org/
- Symposium on the Evolution of Antiviral and Antibacterial Defense: September 4 - 6, 2008. Venue: Berlin, Germany. Website: h t tp: / /www. leopold ina-ef is-e j i -2008.de/ contact.htm.
- Salt & Water Stress in Plants: September 7-12, 2008. Venue: Big Sky Resort, Big Sky, Montana. W e b s i t e : h t t p : / / w w w . g r c . o r g / programs.aspx?year=2008&program=salt.
- Course and Symposium: Microbes and the Law: October 5 - 9, 2008. Venue: Ultuna campus of SLU (Swedish University of Agricultural Sciences) Uppsala, Sweden. Websi te : h t tp : / /www-mik rob .s lu .se / DOMSymposium.
- 2nd ASM Conference on Beneficial Microbes: Beneficial Host-Microbial Interactions: October 12 - 16, 2008. Venue: San Diego, California. Website: http://www.asm.org/ Meetings/index.asp
- APGC Symposium "Plant Functioning in a Changing Global Environment": December 7 – 11, 2008. Venue: University of Melbourne, Melbourne. Website: http://www.apgc.eu.
- Applied & Environmental Microbiology: July 12-17, 2009. Venue: Mount Holyoke College, South Hadley, MA. Website: http://www.grc.org/programs.aspx
- Bacillus-ACT 2009, an ASM Conference: August 30 - September 3, 2009. Venue: Santa Fe, New Mexico (tentative) Website: http://www.asm.org/Meetings/index.asp.
Important E-resources on Microorganisms
Conferences/ Seminars/ Meetings2008 & 2009
ENVIS CENTRE Newsletter Vol.6, No.2 June 2008
EVENTS
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