CHALLENGES OF USING

BENTHIC ASSESSMENTS

IN SAN FRANCISCO ESTUARY

Bruce Thompson and Sarah Lowe

San Francisco Estuary Institute

PURPOSE

• Summarize our understanding of benthic assemblages in the Estuary

Relationships to key abiotic factors:

- Salinity- Sediment-type- Sediment contamination

• Conceptual models of benthic response

• Application of science to benthic assessments

• Information needs: What does RMP need to do?

WHAT IS AN ASSEMBLAGE ?

The group of organisms collected within a common habitat-type; aka community.

• Key attribute is relatively stable species composition and abundances within the assemblage

• Variations may be due to: – life histories – ecological interactions – disturbances

IDENTIFICATION OF ASSEMBLAGES

Multivariate methods were used to determine similarities in species composition and abundances among samples

1. Principal Coordinates Analysis

– Relationships among samples along environmental gradients

2. Classification (Cluster) Analysis

– Data was edited, transformed, and standardized – Bray-Curtis Index: ecological distance, etc. – Clustered sites and species– Produces a dendrogram, and two-way table

DATA USED

Program Dates N. sites N. samples

RMP 1994 – 2001 12 80

BACWA LEMP 1994 – 1997 6 42

BPTCP 1992, 94, 97 22 24

DWR 1994 – 1998 15 436

CISNet 1999 – 2000 6 18

NOAA-EMAP 2000 – 2001 50 50

7 6 5 4 3 2 1 0

OLIGOHALINE MUDDY SEDIMENTS ASSEMBLAGE 192 SAMPLES

OLIGOHALINE SANDY SEDIMENTS ASSEMBLAGE 18 SAMPLES

ESTUARINE TRANSITION SUB-ASSEMBLAGE 72 SAMPLES

POLYHALINE SANDY SEDIMENTS SUB-ASSEMBLAGE 6 SAMPLES

MESOHALINE ASSEMBLAGE 68 SAMPLES

ESTUARINE MARGINS SUB-ASSEMBLAGE 8 SAMPLES -

POLYHALINE MUDDY SEDIMENTS ASSEMBLAGE 60 SAMPLES

ECOLOGICAL DISTANCE

 Oligohaline (muddy) 

Oligohaline-Mesohaline (transition) 

Mesohaline (muddy) 

Polyhaline (muddy)

Major Benthic Assemblages

 Oligohaline (muddy) Oligohaline (sandy)

Oligohaline-Mesohaline (transition) 

Mesohaline (muddy)Mesohaline (margin)

Polyhaline (muddy)Polyhaline (sandy)

Major Assemblage Designations

Species Taxon Muddy Sandy Transition Main Marginsn = 192 18 72 6 68 8 60

Cyprideis sp. A C 15 (27)Manayunkia speciosa P 117 (103)Corbicula fluminea Pe 50 (191) 19 (18) 1 (17)Limnodrilus hoffmeisteri O 36 (180) 1 (5) 2 (10)Varichaetadrilus angustipenis O 30 (188) 1 (12) 1 (19)Corophium spinicorne A 20 (120) 1 (3) 1 (4) 1 (1)Corophium stimpsoni A 57 (162) 2 (12) 4 (19) 1 (1)Gammarus daiberi A 36 (172) 4 (15) 4 (32) 1 (4)Marenzelleria viridis P 6 (70) 2 (11) 20 (57) 2 (21)Corophium alienense A 1 (3) 26 (33) 5 (9) 16 (4) 1 (1)Potamocorbula amurensis Pe 5 (3) 1 (5) 28 (67) 1 (2) 162 (67) 3 (4) 4 (28)Neanthes succinea P 1 (4) 3 (54) 1 (1) 1 (8)Nippoleucon hinumensis T 1 (38) 3 (26) 22 (49) 145 (8) 8 (31)Grandidierella japonica A 1 (6) 1 (9) 4 (29) 46 (6) 3 (19)Gemma gemma Pe 1 (4) 70 (4) 1 (2)Streblospio benedicti P 1 (1) 3 (37) 116 (8) 1 (2)Glycera tenuis P 2 (4)Hesionura coineaui difficilis P 3 (3)Heteropodarke heteromorpha P 18 (4)Corophium spp. A 1 (1) 92 (5) 53 (23)Corophium acherusicum A 1 (1) 1 (17) 6 (1) 745 (34)Ampelisca abdita A 1 (14) 135 (52) 55 (4) 697 (56)Corophium heteroceratum A 1 (7) 9 (42) 133 (55)Tubificidae O 1 (5) 1 (3) 3 (13) 404 (4) 9 (54)Nematoda N 8 (3) 1 (2) 37 (4) 25 (53)Mediomastus spp. P 1 (1) 1 (1) 1 (3) 37 (52)Euchone limnicola P 1 (1) 58 (26)

Mean No. Taxa 13 4 4 7 10 16 36Mean Tot. Abundance 443 33 89 38 362 1130 2110Mean Biomass - - 3.05 0.18 42.2 - 9.91

MuddyOligohaline Estuarine Polyhaline Polyhaline Mesohaline

Sandy

Most Common and Abundant Bay Benthosmean abund. per sample (frequency)

Abiotic Variable

n Axis 1 Axis 2 Axis 3

Salinity 336 .808** -.123* -.072 Temperature 306 -.113* .061 .074 Depth 284 .176** .164 -.544** % Sand 422 -.062 -.121* -.558** % Fines 422 .047 .122* .555** % Gravel 422 .306** .002 -.151** TOC 419 -.496** .346** .390** TSS 52 -.572** -.538** .550** mERMq 115 .350** .262** .278** Dflow 394 -.009 -.031 -.081 Dissolved O2 58 .112 -.126 -.145

ABIOTIC VARIABLESTHAT INFUENCE ASSEMBLAGES

Main Mesohaline

Oligohaline muddy

CONCEPTUAL MODELS OFBENTHIC RESPONSE

• Expected field responses for response to contaminant mixtures by:

– Number of Species, Abundances, Biomass– Higher Taxa (e.g. amphipods)– Sensitive and Tolerant Taxa

• Interactions of key abiotic factors (e.g.salinity, TOC, grain-size)

• Biological and ecological mechanisms

• Guides development of assessment methods

Sediment Contamination / TOC Gradient

Sen

sitiv

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Tol

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xa

CONCEPTUAL MODEL

• Based on Pearson-Rosenberg response model• Response to contamination is similar to TOC• Position along gradient differs among assemblages

Sensitive taxa

Species, Abundances, Biomass Tolerant taxa, Higher taxa

HYPOTHESIZED MECHANISMS

• Interactions of toxicity and TOC enrichment affect taxa with varying tolerances, affects ecological interactions

• Contamination, TOC, and physical disturbance have similar effects on assemblages.

• Low contamination,TOC: - Sensitive taxa abundant, few tolerant/opportunists (t-o)

• Moderate contamination,TOC: - Sensitive taxa decrease due to toxicity - t-o taxa increase (persist) due to increased organic material,

below most toxic thresholds

• High contamination TOC: - Sensitive taxa absent due to acute toxicity - t-o taxa reduced, most effects thresholds exceeded

• Extremely high contamination:

- Acutely toxic to all organisms

1. Evaluation of benthic indicator metrics: What do they indicate?

2. Identification of “reference” samples 3. Evaluation of assessment results: Do results properly

reflect reference and impacted conditions?

KEY ISSUES

DEVELOPMENT OF

BENTHIC ASSESSMENTS METHODS

A) Partial Coefficients Independent Variables Prop. R2 from Candidate Indicator Salinity Fines TOC mERMq Total R2 mERMq Log number of taxa 0.006 0.191A 0.026 0.589* 0.679* 0.87 Log total abundance 0.024 0.068 A <.001 0.394* 0.449* 0.88 Log number amphipod taxa 0.094 0.066A 0.018A 0.332* 0.445* 0.75 Oligochaete abundance 0.042 0.021A 0.007 0.030L 0.095 0.32 Log C. capitata abundance 0.075 0.026 A 0.001 0.028 0.125* 0.22 B) No. taxa 0.140 0.016A 0.332A 0.081* 0.481* 0.17 Total abundance 0.087 0.005A 0.431A 0.078L 0.525* 0.15 Number molluscan taxa 0.047L 0.006A 0.215 0.150* 0.368* 0.41 Oligochaete abundance 0.028 0.052 0.158 0.825* 0.865* 0.95 S. benedicti abundance 0.027L <0.001A 0.541 0.197* 0.642* 0.31

EVALUATION OF CANDIDATE INDICATOR METRICS

REFERENCE SITES

1. Reference samples

• Not toxic• Mostly sensitive species• Oligochaete proportion

2. Reference ranges

Assessment Assemblage Indicator Polyhaline muddy Mesohaline

No. Taxa 21 - 66 6 - 18Tot. Abund. 97 - 2931 20 - 1090Molluscan Taxa 1 - 4 Amphipod Taxa 2 - 11 Oligochaete abund. 0 - 47C. capitata 0 - 13 Streblospio benedicti 0 - 38

Site Date N. Taxa Total Abundance Amphipod Taxa C. capitata AV

BB15 2/15/1994 24 81 0 1 2

EBMUD4 9/23/1994 60 4866 11 16 2

ZM-2 12/3/1997 0 0 0 0 4*

EXAMPLE OF BENTHIC ASSESSMENTPolyhaline Muddy Assemblage

EVALUATION OF ASSESSMENT METHOD

A) Polyhaline Assemblage Reference (n) Impacted (n) Probability

Sediment Contamination (mERMq) 0.0800 (19) 0.3491 (9) 0.013*Total Organic Carbon (%) 0.86 (20) 1.08 (9) 0.131Fine Sediments (% silt+clay) 58.5 (20) 80.8 (9) 0.013*Salinity (psu) 27.3 (19) 28.8 (9) 0.942Sediment Toxicity (percent of samples)0 (20) 100 (4) not tested

B) Mesohaline Assemblage

Sediment Contamination (mERMq) 0.0694 (8) 0.3190 (16) 0.011*Total Organic Carbon (%) 0.91 (9) 2.46 (16) 0.004*Fine Sediments (% silt+clay) 63.6 (9) 85.2 (16) 0.255Salinity (psu) 22.2 (9) 23.6 (12) 1.0Sediment Toxicity (percent of samples)0 (9) 85.7 (14) not tested

CONCLUSIONS

• We know the species composition and abundances in the major benthic assemblages in the Estuary.

• We have a basic understanding of the spatial and temporal scales of change in these assemblages

• Benthic assessment methods exist and have been shown to accurately distinguish reference from impacted benthic conditions and reflect increasing sediment contamination

• Most benthic impacts in SF Estuary occur near the Estuary margins

INFORMATION NEEDS

• Develop benthic assessment methods for other assemblages: mesohaline, oligohaline Delta, wetlands

• Which contaminant(s) cause observed benthic impacts?

• Investigate contaminant specific responses in species composition

• Better links between sediment toxicity and benthic response

SUGGESTED RMP PROPOSALS

1. Include benthos in RMP status and trends program in collaboration with other programs

2. Conduct special studies to identify causes of observed benthic impacts

• multivariate analysis of existing data• lab, field, mesocosm experimental studies