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DOE OSTI2023

Community size-spectra applied to recreational freshwater fisheries in Puerto Rican reservoirs

We developed a management framework based on community size-spectra (CSS) to establish targets to maximize desirable gamefish. We evaluated the influence of relative abundance of fish functional groups and watershed characteristics on the slope of the CSS or ecological efficiency. Both ecological efficiency and capacity were strongly influenced by relative abundance of fish functional groups and the degree of water level variation. Steeper slopes indicated overfished gamefish populations, whereas flatter slopes indicated systems dominated by undesirable invasive large-bodied low trophic position fish. We hypothesize that a desirable fishery would have a target range of CSS slopes that provides a deterministic community-based framework of predictable responses to environmental and food web changes that can be used to evaluate outcomes of management actions and a means to assess annual progress toward desirable conditions.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Factors affecting powerhouse passage of spring migrant smolts at federally operated hydroelectric dams of the Snake and Columbia rivers

From 2008 to 2018, acoustic telemetry studies were conducted to evaluate dam passage survival of spring migrant Chinook salmon and steelhead smolts at seven of the eight federally operated dams on the lower Snake and Columbia rivers. Data from over 87 000 dam passage events were evaluated using regression modeling to identify the effect of spill operations, environmental conditions, and fish characteristics on powerhouse passage probability. In general, powerhouse passage was positively correlated with discharge, negatively correlated with forebay temperature and fish size, and higher for fish that passed the dam at night and for those that approached from the powerhouse side of the river, suggesting powerhouse passage is largely a function of smolt activity level and swimming ability. As such, spilling large volumes of water to reduce powerhouse passage is likely to be most effective during times of reduced activity and swimming ability (e.g., at night, high flows, and cold temperatures). This information can be used to develop dam- and time-specific spill operations that optimize smolt passage, power generation, and other competing demands, such as adult passage.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Fishway Entrance Palisade

This technical report summarizes work that was conducted by the University of Massachusetts Amherst and the U.S. Geological Survey, along with other project partners, on the Fishway Entrance Palisade, a project funded through the Department of Energy’s (DOE) funding opportunity titled ‘Innovative Solutions for Fish Passage at Hydropower Dams’ (DE-FOA-0001662). The period of performance spanned from September 1, 2018 through September 30, 2021. The Entrance Palisade is a novel fish passage engineering technology designed to provide more favorable entry conditions for fish into fishways and to reduce costs relative to conventional fishway auxiliary water systems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Machine learning analysis reveals relationship between pomacentrid calls and environmental cues

Sound production rates of fishes can be used as an indicator for coral reef health, providing an opportunity to utilize long-term acoustic recordings to assess environmental change. As acoustic datasets become more common, computational techniques need to be developed to facilitate analysis of the massive data files produced by long-term monitoring. Machine learning techniques demonstrate an advantage in the identification of fish sounds over manual sampling approaches. Here we evaluated the ability of convolutional neural networks to identify and monitor call patterns for pomacentrids (damselfishes) in a tropical reef region of the western Pacific. A stationary hydrophone was deployed for 39 mo (2014-2018) in the National Park of American Samoa to continuously record the local marine acoustic environment. A neural network was trained—achieving 94% identification accuracy of pomacentrids—to demonstrate the applicability of machine learning in fish acoustics and ecology. The distribution of sound production was found to vary on diel and interannual timescales. Additionally, the distribution of sound production was correlated with wind speed, water temperature, tidal amplitude, and sound pressure level. This research has broad implications for state-of-the-art acoustic analysis and promises to be an efficient, scalable asset for ecological research, environmental monitoring, and conservation planning.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Estimating carrying capacity for juvenile salmon using quantile random forest models

Abstract Establishing robust methods and metrics to evaluate habitat quality is critical for the recovery of endangered Pacific salmonids ( Oncorhynchus spp.). A variety of modeling approaches are used for status and trend monitoring of anadromous species throughout the Pacific Northwest, USA, but current methods may fail to capture the complex relationship between fish and habitat and are often limited in predictive power beyond specific watersheds. Further, the focus on species distribution and abundance is not easily manipulated to predict carrying capacity and traditional stock‐recruitment analyses are reliant on long‐term data which are not always available. In this study, we developed a quantile random forest model to provide estimates of habitat carrying capacity for Chinook salmon ( O. tshawytscha ) parr during the summer months, at both the site and watershed scale. Quantile random forest models allow for the consideration of noisy data, correlated variables, and non‐linear relationships: common features in fish–habitat datasets. We leveraged Columbia Habitat Monitoring Program data to select habitat co‐variates and predict capacity at those sites. We also identified a set of globally available attributes to extrapolate capacity estimate predictions throughout wadeable streams within the Columbia River basin. Total capacity estimates for watersheds closely matched estimates from alternative fish productivity models. Carrying capacity estimates based on quantile random forest models, like those presented here, provide managers a framework to guide the identification, prioritization, and development of habitat rehabilitation actions to recover salmon populations.

See, Kevin E.↗

DOE OSTI2020

Detection and classification capabilities of two multibeam sonars

Multibeam sonars can be used to detect and classify marine fauna under conditions when optical sensors are ineffective. In this work, we compare the detection and classification capabilities of two multibeam sonars with different operating frequencies, the Tritech Gemini 720is (720 kHz) and the Teledyne BlueView M900-2250 (2250 kHz). The two sonars were deployed with overlapping swaths in a narrow tidal channel with peak currents of approximately 2 m/s where seals, schools of fish, and diving birds were intermittently present. In comparing data concurrently acquired by both sonars, we observe differences in the appearance of detected targets and detection capabilities. The detected target tracks are classified using a random forest model as either individual biological targets (flora and fauna, including fish, diving birds, seals, and plant matter), fish schools, or nonbiological targets (including entrained air and sonar artifacts). Despite the observed differences in detection capabilities for the two sonars, automatic classification distinguishes between target classes with precision and recall above 0.7 and 0.9, respectively. Furthermore, these results suggest that while similar methodologies can be used for data analysis, some outcomes from environmental studies using multibeam sonars may be instrument-specific.

16 TIDAL AND WAVE POWER↗

DOE OSTI2020

Understanding Life History Diversity of a Wild Steelhead Population and Managing for Resiliency

Abstract Diversity in steelhead Oncorhynchus mykiss (anadromous Rainbow Trout) is often characterized by varying time spent in freshwater and saltwater environments. However, ontogenetic shifts are not often highlighted as an important diversity characteristic in salmonids. Larger water bodies can play a key role in population stability by buffering limited resources in smaller tributary systems. Based on freshwater and saltwater ages of adult steelhead in Fish Creek, Idaho, there were 12 different life history trajectories observed. Juvenile abundance varied from 12,083 (SE = 1,225.7) to 62,463 (SE = 1,753.8), with ages ranging from young of the year (age 0) to 4 years. Adult abundance fluctuated from 17 (SE < 0.1) to 499 (SE = 67.1), and total age of adults varied from 3 to 7 years. Diversity was most evident in juvenile movement and rearing strategies. We observed four types of movement and rearing pathways in which juveniles either directly migrated to the ocean from Fish Creek or resided for up to three winters in main-stem river habitat in the Clearwater River basin prior to ocean migration. Most juveniles emigrated in the fall at age 2, and most ocean-emigrating smolts were age 3. Subsequently, most juveniles resided for at least one additional winter period before ocean migration. Juvenile diversity was also reflected in adult ages; the mean proportion that spent 3 years in freshwater was 0.55 (SE = 0.03), and the mean proportion that spent 2 years in freshwater was 0.41 (SE = 0.03). Adult sex ratio was female biased (mean ± SE = 0.66 ± 0.02), with a higher proportion of females (0.89 ± 0.03) than males (0.65 ± 0.05) residing in the ocean for at least 2 years. Density-dependent mechanisms were evident in juvenile rearing habitat in Fish Creek for cohorts of high female abundance. Population productivity potentials can be met when tributary and main-stem rearing habitat can be utilized, and this will be essential in attaining recovery goals.

Dobos, Marika E.↗

DOE OSTI2021

Using a Customized Portable Deepwater Portable Electrofisher to Assess Larval Lamprey Populations in Irrigation Canals

Larval lamprey densities were quantified at two large-scale water diversions facilities located on the Yakima River near the city of Yakima, Washington. Water diversions are very common in the Yakima River Basin and provide water to irrigate a diverse range of valuable cropland. Out-migrating larval Pacific Lamprey are vulnerable to entrainment through fish protection screens during the withdrawal period and desiccation or predation during dewatering at the end of the season. In order to determine the impact to lamprey populations which inhabit these regions a portable deepwater electroshocking system was utilized to determine lamprey densities which could otherwise not be determined due to water depth. Surveys were conducted in the fall during the dewatering period in 2015 and 2017 and larval lamprey densities ranged from 0.8 to 8.8 fish m-2 at the Sunnyside Diversion Facility to 4.2 to 6.5 fish m-2 at the Wapato Diversion Facility. The estimates for the total lamprey numbers at each of the region using a portable deepwater electrofishing platform (PDEP) was very similar to those estimates using backpack electrofishing post-dewatering; the PDEP method was 12- 36% higher where comparisons were available. During 2017, the estimated lamprey entrainment at the Sunnyside Diversion increased by 484% from August to November. Lamprey lengths were also determined and ranged from 50 to 130 mm. Our results indicate that the use of the deepwater shocking system was very safe and effective at determining larval lamprey densities at hard to sample regions which are present near irrigation facilities.

larval lamprey, electrofishing, water diversion↗

DOE OSTI2021

Characteristics of an Introduced Walleye Population with Implications for Suppression

Abstract The management of introduced fishes, including Walleye Sander vitreus, whether for control or enhancement, requires understanding of population dynamics at the invasion front. Walleye recently established in the Pend Oreille basin, Idaho, threaten the existing salmonid-based fish community and associated recreational fishery. Therefore, the objectives of this study were to describe population growth and associated life history characteristics. Walleye were sampled in October of 2011, 2014, and 2017 using a standardized gill netting survey protocol to describe trends in relative abundance and evaluate population dynamics. Relative abundance increased exponentially from 1.4 to 4.3 fish/net over the 6-year monitoring period. This population was characterized by fast somatic growth, robust body condition, and early age at maturity at or near the biological maxima for Walleye. Among the survey years, mean length at age 2 varied for female (359–441 mm) and male (358–426 mm) Walleye and relative weight varied from 91 to 98. The sampled Walleye matured at 1 to 4 years of age, and recruitment became more consistent as abundance increased. These density-dependent metrics suggest that the Walleye population is still at low density relative to carrying capacity. The information that was gained from this study was used to better understand potential risks and guide management decisions related to experimental population suppression that is now underway. Suppression under these conditions must overcome the recruitment capabilities of the population. We conclude that natural mortality is likely regulated by density-dependent processes. Therefore, at current (low) density, fishing mortality may be entirely additive and compensation is unlikely to further complicate management.

Ryan, Robert G.↗

DOE OSTI2021

Grandparent Inference from Genetic Data: The Potential for Parentage-Based Tagging Programs to Identify Offspring of Hatchery Strays

Abstract Fisheries managers routinely use hatcheries to increase angling opportunity. Many hatcheries operate as segregated programs where hatchery-origin fish are not intended to spawn with natural-origin conspecifics in order to prevent potential negative effects on the natural-origin population. Currently available techniques to monitor the frequency with which hatchery-origin strays successfully spawn in the wild rely on either genetic differentiation between the hatchery- and natural-origin fish or extensive sampling of fish on the spawning grounds. We present a method to infer grandparent–grandchild trios by using only genotypes from two putative grandparents and one putative grandchild. We developed estimators of false-positive and false-negative error rates and showed that genetic panels containing 500–700 single-nucleotide polymorphisms or 200–300 microhaplotypes are expected to allow application of this technique for monitoring segregated hatchery programs. We discuss the ease with which this technique can be implemented by pre-existing parentage-based tagging programs and provide an R package that applies the method.

Delomas, Thomas A. (ORCID:000000015154759X)↗

DOE OSTI2022

Improving Abundance Estimates of Spring–Summer Snake River Chinook Salmon for Fisheries Management

Abstract The Columbia River basin is home to a run of spring–summer Chinook Salmon Oncorhynchus tshawytscha that returns to the Snake River drainage of Idaho, Oregon, and Washington in the Pacific Northwest. Historically, the run was one of the more productive throughout the Columbia River basin. However, Snake River spring–summer Chinook Salmon have experienced declines in abundance due to overfishing, habitat degradation, and dams. Several stocks are listed as threatened under the U.S. Endangered Species Act and are supported by mitigation hatcheries funded by Idaho Power Company, the Lower Snake River Compensation Plan, and the Bonneville Power Administration. To maximize tribal and state harvest of returning hatchery adults, minimize impacts on wild fish, and ensure that enough hatchery fish return to meet broodstock needs, careful fisheries management is required. Since 2008, managers have used hatchery adults, PIT-tagged as juveniles and detected at Lower Granite Dam, to generate adult abundance estimates. In season, these estimates inform state and tribal harvest shares and ensure that broodstock needs are met. Postseason, they provide smolt-to-adult survival and return rates. Since 2012, parentage-based tagging (PBT) has provided an alternative method to estimate stock- and age-specific returns at Lower Granite Dam, since returning hatchery adults sampled at Lower Granite Dam can be assigned to their parents. We compared stock-specific abundance estimates between PIT- and PBT-derived methodologies for return years 2016–2019. Across all years, PIT tag estimates accounted for 65% of the PBT-based estimates at Lower Granite Dam across all age-groups and release sites combined. This underrepresentation across all groups equated to 49,833 fish that were not accounted for in PIT tag abundance estimates. It is clear that PBT-based estimates should aide in-season harvest management and postseason run reconstruction to avoid the known bias of estimates from PIT tags, especially during years of low returns when increased accuracy is critical.

Coykendall, D. Katharine (ORCID:0000000211482397)↗

DOE OSTI2023

Effects of Livestock Exclusion on Stream Habitat and Aquatic Biota: A Review and Recommendations for Implementation and Monitoring

Abstract To inform riparian restoration, research, and monitoring and to provide management recommendations, we reviewed published studies evaluating the physical and biological effectiveness of livestock exclusion and grazing reduction on various metrics in riparian and aquatic areas. We identified 95 North American studies that reported the effects of livestock grazing reduction on physical habitat (channel morphology, mesohabitats, substrate, and bank stability), biological assemblages (riparian vegetation, macroinvertebrates, fish, and birds), and water quality metrics (temperature, nitrates, phosphorus, and turbidity). Most studies reported that methods to reduce or exclude livestock decreased channel width, width-to-depth ratio, bank erosion, soil bulk density, bare ground, water temperature, nitrogen, and phosphorus and increased riparian vegetation (cover, height, productivity, biomass, and abundance), riparian bird abundance, and young-of-the-year fishes. Results for channel depth, instream substrate, mesohabitats, water depth, juvenile and adult fishes, and macroinvertebrates showed no consistent response to exclusion. Project success was influenced by the time since exclusion; whether there was complete exclusion or continued grazing; and local climate, geology, and soils. Apart from bank erosion and stability, most of the physical and biological metrics took more than a decade to respond to livestock exclusion. However, coupling exclusion with planting and other restoration measures decreased the recovery time. Complete exclusion of livestock produced more consistent improvements in riparian condition and other metrics than rest–rotation or other grazing management strategies. Understanding how physical and biological metrics respond to livestock exclusion will require (1) focused, long-term studies using before–after or before–after, control–impact designs; and (2) monitoring of metrics that most consistently respond to exclusion. Ultimately, the design of exclusions should be driven by local climate, geology, biophysical conditions, and management history. Our results highlight the need for watershed-scale approaches to excluding livestock from broad areas and the need for implementation monitoring to ensure that fencing and other exclusion measures continue to exclude livestock and produce the desired responses.

Krall, Michelle↗

DOE OSTI2021

Importance of Depth and Artificial Structure as Predictors of Female Red Snapper Reproductive Parameters

Abstract The Red Snapper Lutjanus campechanus is a structure‐associated species occurring across a wide depth range in the northern Gulf of Mexico. We used the random forest machine learning algorithm to understand which habitat and individual fish characteristics could predict reproductive parameters of female Red Snapper. We evaluated fish captured from 2016 to 2018 on three artificial structure types with various structure heights at depths of 100 m or less. Overall, we found that depth and month were important predictors for most reproductive parameters, but the type of structure (artificial reefs, oil platforms, and rigs‐to‐reefs structures) was not important. Maturity was correctly classified in 88.9% of the cases when using the random forest ensemble model, with important predictors including FL, depth, structure height, and month of collection. Spawning seasonality (measured as gonadosomatic index [GSI]) was correctly classified in 59.5% of the cases when using histology reproductive phase, FL, month, and depth variables. Reproductively active or inactive females were correctly classified in 89.3% of the cases using GSI, month, FL, and depth, while females in the developing versus spawning capable phases were correctly classified in 82.2% of the cases using GSI, FL, month, and depth. Histological indicators that show potential spawning within a 36‐h period were correctly classified 61.5% of the time, with the best predictors being depth, FL, GSI, and month. Stepwise regression indicated that month was the only factor that significantly predicted contrasts in relative batch fecundity, with significantly greater values in August compared to all other months. Our findings suggest that female Red Snapper reproductive effort is not consistently or well predicted by artificial structure type or height but that a combination of fish FL, month, and depth can predict reproductive characteristics of female Red Snapper.

Brown‐Peterson, Nancy J.↗

DOE OSTI2023

The effect of reducing dietary lipid and food availability on precocious male maturation in Chinook Salmon: A production-scale hatchery experiment

Abstract Objective Age of maturation in Chinook Salmon Oncorhynchus tshawytscha is phenotypically plastic, influenced by both genotype and environmental factors, including the availability and composition of the diet. Salmon hatchery programs often rear fish under accelerated growth regimes using high-lipid diets that can result in earlier age at maturity, including increased prevalence of age-2 males (minijacks). The goal of this investigation was to compare alternative dietary regimes to mitigate for this shift in age at maturity in hatchery-reared Umatilla River fall Chinook Salmon. Methods Juvenile fish were reared at Bonneville Hatchery, Oregon, under four dietary treatments across four replicate brood years. Dietary treatments included two feeding frequencies (standard [fed 7 days/week] and reduced [fed 4 days/week]) and two dietary lipid levels (standard [18%] and reduced [12%]) in a 2 × 2 factorial design. Dietary treatments were applied for approximately 9 months, beginning in March (a month after fry emergence) and lasting until December of the first year, after which all fish were reared on the standard feeding regime (7 days–18%) until the time of release the following spring as yearlings. Result We observed significant interannual variation in the proportion of minijacks produced among dietary treatments. For all brood years, decreasing the feeding frequency from 7 to 4 days/week reduced the proportion minijacks by 35.9%, and lowering dietary lipid from 18% to 12% reduced the proportion minijacks by 30%. The combined effects of reducing the feeding frequency and lowering dietary lipid were additive, reducing the proportion minijacks by 65.5% compared to the standard rearing regime. Growth and energetic indices were monitored throughout and confirmed findings from previous laboratory-based studies indicating that physiological status 10–12 months prior to spawn timing is important for the “decision” to mature. Conclusion Results of this investigation provide useful insights for optimizing rearing regimes for the Umatilla River program and other Chinook Salmon hatchery programs.

Harstad, Deborah L. (ORCID:0000000202676085)↗

DOE OSTI2023

Effects of volitional emigration timing and smolt size on survival and age-at-return in a Pacific salmon hatchery population

Abstract Many Pacific salmon populations are returning from sea at younger ages and smaller sizes. Hatchery culture, management practices, and environmental factors influence juvenile release size and emigration timing, which in turn affect important demographic characteristics in returning adults. We analyzed data from approximately 345,000 tagged spring Chinook Salmon juveniles exiting Cle Elum Supplementation and Research Facility (Yakima River, Washington, USA) acclimation sites over thirteen brood years (2002–2014), evaluating smolt size, emigration timing, river flow, juvenile survival, and age-at-return. We observed a relationship between size and volitional exit timing of smolts from acclimation sites, with larger fish tending to emigrate earlier than smaller fish. Early emigration was also coincident with lower river flows near acclimation sites. Later emigration timing was correlated with an increase in apparent survival of juveniles to Bonneville Dam (500–530 km downstream of acclimation sites), but also with a lower rate of survival to return from sea. In general, for juveniles successfully emigrating downstream of Bonneville Dam, age-at-return increased with decreasing juvenile fish size and later emigration timing. Our results support a growing body of evidence that hatchery practices may result in larger smolts that tend to return at younger ages. Given the biological and economic consequences of younger age-at-maturation, methods to reverse this trend should be further explored and implemented.

Bosch, William J. (ORCID:0000000300447390)↗

DOE OSTI2022

Computational studies of hydraulic stressors for biological performance assessment in a hydropower plant with Kaplan turbine

We report Hydropower is currently one of the preeminent sources of renewable energy in the United States and globally. Hydropower plants also have detrimental impacts on the environment and ecology, including direct impacts to anadromous fish populations. The computational fluid dynamics (CFD) – based Biological Performance Assessment (BioPA) toolset is used for biological evaluations of fish passage through hydropower plants. The hydraulic environment of a hydropower plant was evaluated using CFD coupled with discrete element method (DEM) simulations. The predicted flow field and particle collision rate were validated against the experimental data in a water flume that has an idealized hydroturbine distributor geometry. Flow simulations were conducted to evaluate the hydraulic stressors, such as nadir pressure, fluid shear, runner collision, in a physical scale in a hydropower plant with Kaplan turbine which are responsible for injury and mortality of fish in a downstream migration. The cumulative exposure probability for the nadir pressure and collision with turbine runner was found to decrease with increased discharge rate. The lowest discharge rate shows the higher value of cumulative shear exposure probability. The maximum value of collision velocity increases with increased discharge rate. We offer the conclusions that will help in understanding various hydraulic stressors for biological assessment for environmentally sustainable hydroturbine passage.

13 HYDRO ENERGY↗

DOE OSTI2020

Brown watersnakes (Nerodia taxispilota) as bioindicators of mercury contamination in a riverine system

Herein, mercury (Hg) is a contaminant that enters the environment through natural or anthropogenic means. Ecological risk assessments have examined Hg bioaccumulation and effects in many taxa, but little is known about Hg dynamics in reptiles, or their potential use as bioindicator species for monitoring Hg in aquatic systems. Numerous snake species, like North American watersnakes (Nerodia spp.), are piscivorous and are exposed to Hg through their diet. The purpose of this study was to identify factors associated with Hg accumulation in a common watersnake species and compare Hg concentrations of the snakes to those in fish occupying the same habitats. To this end, we sampled brown watersnakes (Nerodia taxispilota) from the Savannah River, a major river system in the southeastern U.S., and compared N. taxispilota Hg accumulation trends to those of bass (Micropterus salmoides), catfish (Ictalurus and Ameiurus spp.), and panfish (Lepomis and Pomoxis spp.) collected from the same reach. Total Hg (THg) in N. taxispilota tail tips ranged from 0.020 to 0.431 mg/kg (wet weight; mean: 0.104 ± 0.008). Snake tail THg was significantly correlated with blood THg, which ranged from 0.003 to 1.140 mg/kg (0.154 ± 0.019). Snake size and site of capture were significantly associated with tail THg. Snake tail THg increased at sites along and downstream of the area of historic Hg pollution, consistent with fish THg. Snake muscle THg was predicted based on tail THg and ranged from 0.095 to 1.160 (0.352 ± 0.022). To gauge Hg biomagnification in N. taxispilota, we compared predicted snake muscle THg concentrations to THg in fish of consumable size. Average biomagnification factors for THg in N. taxispilota were 3.1 (panfish) and 5.4 (catfish), demonstrating N. taxispilota likely biomagnify Hg through their diet. These results reveal N. taxispilota to be an effective bioindicator species for monitoring Hg in aquatic environments.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Experimentally-validated correlation analysis reveals new anaerobic methane oxidation partnerships with consortium-level heterogeneity in diazotrophy

Abstract Archaeal anaerobic methanotrophs (“ANME”) and sulfate-reducing Deltaproteobacteria (“SRB”) form symbiotic multicellular consortia capable of anaerobic methane oxidation (AOM), and in so doing modulate methane flux from marine sediments. The specificity with which ANME associate with particular SRB partners in situ, however, is poorly understood. To characterize partnership specificity in ANME-SRB consortia, we applied the correlation inference technique SparCC to 310 16S rRNA amplicon libraries prepared from Costa Rica seep sediment samples, uncovering a strong positive correlation between ANME-2b and members of a clade of Deltaproteobacteria we termed SEEP-SRB1g. We confirmed this association by examining 16S rRNA diversity in individual ANME-SRB consortia sorted using flow cytometry and by imaging ANME-SRB consortia with fluorescence in situ hybridization (FISH) microscopy using newly-designed probes targeting the SEEP-SRB1g clade. Analysis of genome bins belonging to SEEP-SRB1g revealed the presence of a complete nifHDK operon required for diazotrophy, unusual in published genomes of ANME-associated SRB. Active expression of nifH in SEEP-SRB1g within ANME-2b—SEEP-SRB1g consortia was then demonstrated by microscopy using hybridization chain reaction (HCR-) FISH targeting nifH transcripts and diazotrophic activity was documented by FISH-nanoSIMS experiments. NanoSIMS analysis of ANME-2b—SEEP-SRB1g consortia incubated with a headspace containing CH4 and 15N2 revealed differences in cellular 15N-enrichment between the two partners that varied between individual consortia, with SEEP-SRB1g cells enriched in 15N relative to ANME-2b in one consortium and the opposite pattern observed in others, indicating both ANME-2b and SEEP-SRB1g are capable of nitrogen fixation, but with consortium-specific variation in whether the archaea or bacterial partner is the dominant diazotroph.

58 GEOSCIENCES↗