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DOE OSTI2024

Biogeochemical and community ecology responses to the wetting of non-perennial streams

Transitions between dry and wet hydrologic states are the defining characteristic of non-perennial rivers and streams, which constitute the majority of the global river network. Although past work has focused on stream drying characteristics, there has been less focus on how hydrology, ecology and biogeochemistry respond and interact during stream wetting. Wetting mechanisms are highly variable and can range from dramatic floods and debris flows to gradual saturation by upwelling groundwater. This variation in wetting affects ecological and biogeochemical functions, including nutrient processing, sediment transport and the assembly of biotic communities. Here, in this work, we synthesize evidence describing the hydrological mechanisms underpinning different types of wetting regimes, the associated biogeochemical and organismal responses, and the potential scientific and management implications for downstream ecosystems. This combined multidisciplinary understanding of wetting dynamics in non-perennial streams will be key to predicting and managing for the effects of climate change on non-perennial ecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Solutions in microbiome engineering: prioritizing barriers to organism establishment

Abstract Microbiome engineering is increasingly being employed as a solution to challenges in health, agriculture, and climate. Often manipulation involves inoculation of new microbes designed to improve function into a preexisting microbial community. Despite, increased efforts in microbiome engineering inoculants frequently fail to establish and/or confer long-lasting modifications on ecosystem function. We posit that one underlying cause of these shortfalls is the failure to consider barriers to organism establishment. This is a key challenge and focus of macroecology research, specifically invasion biology and restoration ecology. We adopt a framework from invasion biology that summarizes establishment barriers in three categories: (1) propagule pressure, (2) environmental filtering, and (3) biotic interactions factors. We suggest that biotic interactions is the most neglected factor in microbiome engineering research, and we recommend a number of actions to accelerate engineering solutions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA

Late Pliocene and Early Pleistocene epochs 3.6 to 0.8 million years ago had climates resembling those forecasted under future warming. Palaeoclimatic records show strong polar amplification with mean annual temperatures of 11–19 °C above contemporary values. The biological communities inhabiting the Arctic during this time remain poorly known because fossils are rare. Here we report an ancient environmental DNA (eDNA) record describing the rich plant and animal assemblages of the Kap København Formation in North Greenland, dated to around two million years ago. The record shows an open boreal forest ecosystem with mixed vegetation of poplar, birch and thuja trees, as well as a variety of Arctic and boreal shrubs and herbs, many of which had not previously been detected at the site from macrofossil and pollen records. The DNA record confirms the presence of hare and mitochondrial DNA from animals including mastodons, reindeer, rodents and geese, all ancestral to their present-day and late Pleistocene relatives. The presence of marine species including horseshoe crab and green algae support a warmer climate than today. The reconstructed ecosystem has no modern analogue. The survival of such ancient eDNA probably relates to its binding to mineral surfaces. Our findings open new areas of genetic research, demonstrating that it is possible to track the ecology and evolution of biological communities from two million years ago using ancient eDNA.

58 GEOSCIENCES↗
DOE OSTI2020

Columbia River Surface Water and Pore Water Unaligned FTICR-MS Data Associated with “Using Community Assembly Metrics from Metacommunity Ecology to Understand Environmental Metabolomes”

Surface water and pore water samples were collected at five sites along a shoreline transect of the Columbia River, southeastern WA, USA in 2017. This dataset is comprised of (1) high resolution characterization of dissolved organic matter via 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) analyzed through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory) and (2) a metadata csv file. The FTICR-MS files are .xml, and the data package includes instructions for using Formularity (https://omics.pnl.gov/software/formularity) and an R script to process the data based on the user’s specific needs. The data are associated with the publication “Using community assembly metrics from metacommunity ecology to understand environmental metabolomes” that will be published in Nature Communications (Danczak et al.). The study aimed to investigate gaps in understanding the spatiotemporal organization of environmental metabolomes to improve the ability to predict ecosystem function. Associated sequencing data will be published via NCBI. The access information for NCBI and the publication DOI will be added to this abstract when they are available. Please use the data package’s DOI to cite the data package. We ask that you acknowledge the U.S. Department of Energy (DOE) Biological and Environmental Research (BER) Subsurface Biogeochemical Research (SBR) program when using the data. All data are free to be used for any purpose, such as for manuscripts, presentations, and grant proposals. There is no obligation to include data package authors as co-authors.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

A chromosome-level genome assembly of the Chinese cork oak (Quercus variabilis)

Quercus variabilis (Fagaceae) is an ecologically and economically important deciduous broadleaved tree species native to and widespread in East Asia. It is a valuable woody species and an indicator of local forest health, and occupies a dominant position in forest ecosystems in East Asia. However, genomic resources from Q. variabilis are still lacking. Here, we present a high-quality Q. variabilis genome generated by PacBio HiFi and Hi-C sequencing. The assembled genome size is 787 Mb, with a contig N50 of 26.04 Mb and scaffold N50 of 64.86 Mb, comprising 12 pseudo-chromosomes. The repetitive sequences constitute 67.6% of the genome, of which the majority are long terminal repeats, accounting for 46.62% of the genome. We used ab initio , RNA sequence-based and homology-based predictions to identify protein-coding genes. A total of 32,466 protein-coding genes were identified, of which 95.11% could be functionally annotated. Evolutionary analysis showed that Q. variabilis was more closely related to Q. suber than to Q. lobata or Q. robur. We found no evidence for species-specific whole genome duplications in Quercus after the species had diverged. This study provides the first genome assembly and the first gene annotation data for Q. variabilis. These resources will inform the design of further breeding strategies, and will be valuable in the study of genome editing and comparative genomics in oak species.

Han, Biao↗
DOE OSTI2024

Identifying priority ecosystem services in tidal wetland restoration

Classification systems can be an important tool for identifying and quantifying the importance of relationships, assessing spatial patterns in a standardized way, and forecasting alternative decision scenarios to characterize the potential benefits (e.g., ecosystem services) from ecosystem restoration that improve human health and well-being. We present a top-down approach that systematically leverages ecosystem services classification systems to identify potential services relevant for ecosystem restoration decisions. We demonstrate this approach using the U.S. Environmental Protection Agency’s National Ecosystem Service Classification System Plus (NESCS Plus) to identify those ecosystem services that are relevant to restoration of tidal wetlands. We selected tidal wetland management documents from federal agencies, state agencies, wetland conservation organizations, and land stewards across three regions of the continental United States (northern Gulf of Mexico, Mid-Atlantic, and Pacific Northwest) to examine regional and organizational differences in identified potential benefits of tidal wetland restoration activities and the potential user groups who may benefit. We used an automated document analysis to quantify the frequencies at which different wetland types were mentioned in the management documents along with their associated beneficiary groups and the ecological end products (EEPs) those beneficiaries care about, as defined by NESCS Plus. Results showed that a top combination across all three regions, all four organizations, and all four tidal wetland types was the EEP naturalness paired with the beneficiary people who care (existence). Overall, the Mid-Atlantic region and the land steward organizations mentioned ecosystem services more than the others, and EEPs were mentioned in combination with tidal wetlands as a high-level, more general category than the other more specific tidal wetland types. Certain regional and organizations differences were statistically significant. Those results may be useful in identifying ecosystem services-related goals for tidal wetland restoration. This approach for identifying and comparing ecosystem service priorities is broadly transferrable to other ecosystems or decision-making contexts.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Overcoming persistent challenges in putting environmental flow policy into practice: a systematic review and bibliometric analysis

The implementation of environmental flows (e-flows) aims to reduce the negative impacts of hydrological alteration on freshwater ecosystems. Despite the growing attention to the importance of e-flows since the 1970s, actual implementation has lagged. Therefore, we explore the limitations in e-flows implementation, their systemic reasons, and solutions. We conducted a systematic review and a bibliometric analysis to identify peer-reviewed articles published on the topic of e-flows implementation research in the last two decades, resulting in 68 research and review papers. Co-occurrence of terms, and geographic and temporal trends were analyzed to identify the gaps in environmental water management and propose recommendations to address limitations on e-flows implementation. We identify the underlying causes and potential solutions to such challenges in environmental water management. The limitations to e-flow implementation identified were categorized into 21 classes. The most recognized limitation was the competing priorities of human uses of water (n = 29). Many secondary limitations, generally co-occurring in co-causation, were identified as limiting factors, especially for implementing more nuanced and sophisticated e-flows. The lack of adequate hydrological data (n = 24) and ecological data (n = 28) were among the most mentioned, and ultimately lead to difficulties in starting or continuing monitoring/adaptive management (n = 28) efforts. The lack of resource/capacity (n = 21), experimentation (n = 19), regulatory enforcement (n = 17), and differing authorities involved (n = 18) were also recurrent problems, driven by the deficiencies in the relative importance given to e-flows when facing other human priorities. In order to provide a clearer path for successful e-flow implementation, system mapping can be used as a starting point and general-purpose resource for understanding the sociohydrological problems, interactions, and inherited complexity of river systems. Secondly, we recommend a system analysis approach to address competing demands, especially with the use of coupled water-energy modeling tools to support decision-making when hydropower generation is involved. Such approaches can better assess the complex interactions among the hydrologic, ecological, socioeconomic, and engineering dimensions of water resource systems and their effective management. Lastly, given the complexities in environmental water allocation, implementation requires both scientific rigor and proven utility. Consequently, and where possible, we recommend a move from simplistic flow allocations to a more holistic approach informed by hydroecological principles. To ease conflicts between competing water demands, water managers can realize more 'pop per drop' by supporting key components of a flow regime that include functional attributes and processes that enhance biogeochemical cycling, structural habitat formation, and ecosystem maintenance.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Cryptic cycling by electroactive bacterioplankton in Trout Bog Lake

The potential for extracellular electron transfer (EET) is a prevailing genomic feature of humic lake bacterioplankton. However, there has been little evidence for the substantial ecological contribution predicted by genetics. We hypothesized that anoxygenic phototrophic electrotrophs and accompanying heterotrophic electrogens cycle dissolved organic matter (DOM) between oxidized and reduced states. We predicted that such bacterioplankton would exhibit diel-scale oscillations due to the light dependency of photosynthesis. Using Trout Bog Lake in Wisconsin, USA, as our model ecosystem, we profiled the water column with depth-discrete metagenomic, physiochemical, and electrochemical analyses. We observed variation in oxidation reduction potential (ORP) in response to sunlight, initiating at depths populated by anoxygenic phototrophs with EET genes. We developed an automated buoy to measure electric current flow between many pairs of electrodes simultaneously, observing correlation in electron consumption to sunlight. Our results, combined with published metatranscriptomic analysis, indicate the occurrence of electron cycling between phototrophic oxidation (electrotrophic metabolism) by Chlorobium and anaerobic respiration (electrogenic metabolism) by Geothrix, involving DOM. We also repeatedly observed gradual seasonal increases in hypolimnion ORP throughout summer. These diel and seasonal patterns imply that electroactive DOM mediates the ecology of electroactive bacteria in lakes, controlling humic lake methane emissions.IMPORTANCEWe investigated the physical, chemical, and redox characteristics of a bog lake and electrodes hung therein to test the hypothesis that dissolved organic matter is being cycled between oxidized and reduced states by electroactive bacterioplankton powered by phototrophy. To do so, we performed field-based analyses on multiple timescales using both established and novel instrumentation. We paired these analyses with recently developed bioinformatics pipelines for metagenomics data to investigate genes that enable electroactive metabolism and accompanying metabolisms. Our results are consistent with our hypothesis and yet upend some of our other expectations. Our findings have implications for understanding greenhouse gas emissions from lakes, including electroactivity as an integral part of lake metabolism throughout more of the anoxic parts of lakes and for a longer portion of the summer than expected. Our results also give a sense of what electroactivity occurs at given depths and provide a strong basis for future studies.

carbon emissions↗
DOE OSTI2023

Asymmetric response of Amazon forest water and energy fluxes to wet and dry hydrological extremes reveals onset of a local drought-induced tipping point

Understanding the effects of intensification of Amazon basin hydrological cycling—manifest as increasingly frequent floods and droughts—on water and energy cycles of tropical forests is essential to meeting the challenge of predicting ecosystem responses to climate change, including forest “tipping points”. Here, we investigated the impacts of hydrological extremes on forest function using 12+ years of observations (between 2001–2020) of water and energy fluxes from eddy covariance, along with associated ecological dynamics from biometry, at the Tapajós National Forest. Measurements encompass the strong 2015–2016 El Niño drought and La Niña 2008–2009 wet events. We found that the forest responded strongly to El Niño-Southern Oscillation (ENSO): Drought reduced water availability for evapotranspiration ( ET ) leading to large increases in sensible heat fluxes ( H ). Partitioning ET by an approach that assumes transpiration ( T ) is proportional to photosynthesis, we found that water stress-induced reductions in canopy conductance ( G s ) drove T declines partly compensated by higher evaporation ( E ). By contrast, the abnormally wet La Niña period gave higher T and lower E , with little change in seasonal ET . Both El Niño-Southern Oscillation (ENSO) events resulted in changes in forest structure, manifested as lower wet-season leaf area index. However, only during El Niño 2015–2016, we observed a breakdown in the strong meteorological control of transpiration fluxes (via energy availability and atmospheric demand) because of slowing vegetation functions (via shutdown of G s and significant leaf shedding). Drought-reduced T and G s , higher H and E , amplified by feedbacks with higher temperatures and vapor pressure deficits, signaled that forest function had crossed a threshold, from which it recovered slowly, with delay, post-drought. In conclusion, identifying such tipping point onsets (beyond which future irreversible processes may occur) at local scale is crucial for predicting basin-scale threshold-crossing changes in forest energy and water cycling, leading to slow-down in forest function, potentially resulting in Amazon forests shifting into alternate degraded states.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Hyperspectral Reflectance for Measuring Canopy‐Level Nutrients and Photosynthesis in a Salt Marsh

Abstract Salt marsh ecosystems are underrepresented in process‐based models due to their unique location across the terrestrial–aquatic interface. Particularly, the role of leaf nutrients on canopy photosynthesis (F A ) remains unclear, despite their relevance for regulating vegetation growth. We combined multiyear information of canopy‐level nutrients and eddy covariance measurements with canopy surface hyperspectral remote sensing (CSHRS) to quantify the spatial and temporal variability of F A in a temperate salt marsh. We found that F A showed a positive relationship with canopy‐level N at the ecosystem scale and for areas dominated by Spartina cynosuroides , but not for areas dominated by short S. alterniflora . F A showed a positive relationship with canopy‐level P, K, and Na, but a negative relationship with Fe, for areas associated with S. cynosuroides , S. alterniflora , and at the ecosystem scale. We used partial least squares regression (PLSR) with CSHRS and found statistically significant data–model agreements to predict canopy‐level nutrients and F A . The red‐edge electromagnetic region and ∼770 nm showed the highest contribution of variance in PLSR models for canopy‐level nutrients and F A , but we propose that underlying sediment biogeochemistry can complicate interpretation of reflectance measurements. Our findings highlight the relevance of spatial variability in salt marshes vegetation and the promising application of CSHRS for linking information of canopy‐level nutrients with F A . We call for further development of canopy surface hyperspectral methods and analyses across salt marshes to improve our understanding of how these ecosystems will respond to global environmental change.

Environmental Sciences & Ecology↗
DOE OSTI2023

Dinitrogen Emissions Dominate Nitrogen Gas Emissions From Soils With Low Oxygen Availability in a Moist Tropical Forest

Lowland tropical forest soils are relatively N rich and are the largest global source of N 2 O (a powerful greenhouse gas) to the atmosphere. Despite the importance of tropical N cycling, there have been few direct measurements of N 2 (an inert gas that can serve as an alternate fate for N 2 O) in tropical soils, limiting our ability to characterize N budgets, manage soils to reduce N 2 O production, or predict the future role that N limitation to primary productivity will play in buffering against climate change. We collected soils from across macro‐ and micro‐topographic gradients that have previously been shown to differ in O 2 availability and trace gas emissions. We then incubated these soils under oxic and anoxic headspaces to explore the relative effect of soil location versus transient redox conditions. No matter where the soils came from, or what headspace O 2 was used in the incubation, N 2 emissions dominated the flux of N gas losses. In the macrotopography plots, production of N 2 and N 2 O were higher in low O 2 valleys than on more aerated ridges and slopes. In the microtopography plots, N 2 emissions from plots with lower mean soil O 2 (5%–10%) were greater than in plots with higher mean soil O 2 (10%–20%). We estimate an N gas flux of ∼37 kg N/ha/yr from this forest, 99% as N 2 . These results suggest that N 2 fluxes may have been systematically underestimated in these landscapes, and that the measurements we present call for a reevaluation of the N budgets in lowland tropical forest ecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Community Structure and Microbial Associations in Sediment-Free Methanotrophic Enrichment Cultures from a Marine Methane Seep

We report Syntrophic consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) consume large amounts of methane and serve as the foundational microorganisms in marine methane seeps. Despite their importance in the carbon cycle, research on the physiology of ANME-SRB consortia has been hampered by the slow growth and complex physicochemical environment the consortia inhabit. Here, we report successful sediment-free enrichment of ANME-SRB consortia from deep-sea methane seep sediments in the Santa Monica Basin, California. Anoxic Percoll density gradients and size-selective filtration were used to separate ANME-SRB consortia from sediment particles and single cells to accelerate the cultivation process. Over a 3-year period, a subset of the sediment-associated ANME and SRB lineages, predominantly comprised of ANME-2a/2b (“Candidatus Methanocomedenaceae”) and their syntrophic bacterial partners, SEEP-SRB1/2, adapted and grew under defined laboratory conditions. Metagenome-assembled genomes from several enrichments revealed that ANME-2a, SEEP-SRB1, and Methanococcoides in different enrichments from the same inoculum represented distinct species, whereas other coenriched microorganisms were closely related at the species level. This suggests that ANME, SRB, and Methanococcoides are more genetically diverse than other members in methane seeps. Flow cytometry sorting and sequencing of cell aggregates revealed that Methanococcoides, Anaerolineales, and SEEP-SRB1 were overrepresented in multiple ANME-2a cell aggregates relative to the bulk metagenomes, suggesting they were physically associated and possibly interacting. Overall, this study represents a successful case of selective cultivation of anaerobic slow-growing microorganisms from sediments based on their physical characteristics, introducing new opportunities for detailed genomic, physiological, biochemical, and ecological analyses. Biological anaerobic oxidation of methane (AOM) coupled with sulfate reduction represents a large methane sink in global ocean sediments. Methane consumption is carried out by syntrophic archaeal-bacterial consortia and fuels a unique ecosystem, yet the interactions in these slow-growing syntrophic consortia and with other associated community members remain poorly understood. The significance of this study is the establishment of sediment-free enrichment cultures of anaerobic methanotrophic archaea and sulfate-reducing bacteria performing AOM with sulfate using selective cultivation approaches based on size, density, and metabolism. By reconstructing microbial genomes and analyzing community composition of the enrichment cultures and cell aggregates, we shed light on the diversity of microorganisms physically associated with AOM consortia beyond the core syntrophic partners. These enrichment cultures offer simplified model systems to extend our understanding of the diversity of microbial interactions within marine methane seeps.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Long-Term Stochasticity Combines With Short-Term Variability in Assembly Processes to Underlie Rice Paddy Sustainability

Revealing temporal patterns of community assembly processes is important for understanding how microorganisms underlie the sustainability of agroecosystem. The ancient terraced rice paddies at Longji provide an ideal platform to study temporal dynamics of agroecosystem sustainability due to their chronosequential records of soil physicochemistry and well-archived microbial information along 630-year rice cultivation. We used statistical null models to evaluate microbial assembly processes along the soil chronosequences of Longji rice paddies through time. Stochastic and deterministic assembly processes jointly governed microbial community composition within successional eras (less than 250 years), and within-era determinism was mainly driven by soil fertility and redox conditions alone or in combination. Conversely, across successional eras (i.e., over 300 years), stochasticity linearly increased with increasing duration between eras and was eventually predominant for the whole 630 years. We suggest that the impact of stochasticity vs. determinism on assembly is timescale-dependent, and we propose that the importance of stochastic assembly of microbial community at longer timescales is due to the gradual changes in soil properties under long-term rice cultivation, which in turn contribute to the sustainability of paddy ecosystem by maintaining a diverse community of microorganisms with multi-functional traits. In total, our results indicate that knowledge on the timescales at which assembly processes govern microbial community composition is key to understanding the ecological mechanisms generating agroecosystem sustainability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Editorial: Plant-Soil Interactions Under Changing Climate

The health and well-being of plants and soil is crucial for all life on Earth. It is well-known that vegetation cover follows climatic zones, and plants respond to climatic drivers such as temperature and precipitation. It is also well-known that plant health depends on the properties and health of the soil, and that strong interactions among biota above and belowground dictate the functioning of both realms. Yet, soils and the processes occurring belowground are often considered a “black box,” and are treated very simplistically in our efforts to understand, quantify, and model the future of the planet. Our understanding of the interactions between plants and soils is also far from complete and offers some of the most important research frontiers in community ecology, biogeochemistry, and global change science.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Modeling biological nitrogen fixation in global natural terrestrial ecosystems

Biological nitrogen fixation plays an important role in the global nitrogen cycle. However, the fixation rate has been usually measured or estimated at a particular observational site. To quantify the fixation amount at the global scale, process-based models are needed. This study develops a biological nitrogen fixation model to quantitatively estimate the nitrogen fixation rate by plants in a natural environment. The revised nitrogen module better simulates the nitrogen cycle in comparison with our previous model that has not considered the fixation effects. The new model estimates that tropical forests have the highest fixation rate among all ecosystem types, which decreases from the Equator to the polar region. The estimated nitrogen fixation in global terrestrial ecosystems is 61.5 Tg N yr-1 with a range of 19.8–107.9 Tg N yr-1 in the 1990s. Our estimates are relatively low compared to some early estimates using empirical approaches but comparable to more recent estimates that involve more detailed processes in their modeling. Furthermore, the contribution of nitrogen made by biological nitrogen fixation depends on ecosystem type and climatic conditions. This study highlights that there are relatively large effects of biological nitrogen fixation on ecosystem nitrogen cycling. and the large uncertainty of the estimation calls for more comprehensive understanding of biological nitrogen fixation. More direct observational data for different ecosystems are in need to improve future quantification of fixation and its impacts.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom

Background: Lagoons are common along coastlines worldwide and are important for biogeochemical element cycling, coastal biodiversity, coastal erosion protection and blue carbon sequestration. These ecosystems are frequently disturbed by weather, tides, and human activities. Here, we investigated a shallow lagoon in New England. The brackish ecosystem releases hydrogen sulfide particularly upon physical disturbance, causing blooms of anoxygenic sulfur-oxidizing phototrophs. To study the habitat, microbial community structure, assembly and function we carried out in situ experiments investigating the bloom dynamics over time. Results: Phototrophic microbial mats and permanently or seasonally stratified water columns commonly contain multiple phototrophic lineages that coexist based on their light, oxygen and nutrient preferences. We describe similar coexistence patterns and ecological niches in estuarine planktonic blooms of phototrophs. The water column showed steep gradients of oxygen, pH, sulfate, sulfide, and salinity. The upper part of the bloom was dominated by aerobic phototrophic Cyanobacteria, the middle and lower parts by anoxygenic purple sulfur bacteria (Chromatiales) and green sulfur bacteria (Chlorobiales), respectively. We show stable coexistence of phototrophic lineages from five bacterial phyla and present metagenome-assembled genomes (MAGs) of two uncultured Chlorobaculum and Prosthecochloris species. In addition to genes involved in sulfur oxidation and photopigment biosynthesis the MAGs contained complete operons encoding for terminal oxidases. The metagenomes also contained numerous contigs affiliating with Microviridae viruses, potentially affecting Chlorobi. Our data suggest a short sulfur cycle within the bloom in which elemental sulfur produced by sulfide-oxidizing phototrophs is most likely reduced back to sulfide by Desulfuromonas sp. Conclusions: The release of sulfide creates a habitat selecting for anoxygenic sulfur-oxidizing phototrophs, which in turn create a niche for sulfur reducers. Strong syntrophism between these guilds apparently drives a short sulfur cycle that may explain the rapid development of the bloom. The fast growth and high biomass yield of Chlorobi-affiliated organisms implies that the studied lineages of green sulfur bacteria can thrive in hypoxic habitats. This oxygen tolerance is corroborated by oxidases found in MAGs of uncultured Chlorobi. The findings improve our understanding of the ecology and ecophysiology of anoxygenic phototrophs and their impact on the coupled biogeochemical cycles of sulfur and carbon.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

efam: an e xpanded, metaproteome-supported HMM profile database of viral protein fam ilies

Viruses infect, reprogram and kill microbes, leading to profound ecosystem consequences, from elemental cycling in oceans and soils to microbiome-modulated diseases in plants and animals. Although metagenomic datasets are increasingly available, identifying viruses in them is challenging due to poor representation and annotation of viral sequences in databases. Here, we establish efam, an expanded collection of Hidden Markov Model (HMM) profiles that represent viral protein families conservatively identified from the Global Ocean Virome 2.0 dataset. This resulted in 240 311 HMM profiles, each with at least 2 protein sequences, making efam >7-fold larger than the next largest, pan-ecosystem viral HMM profile database. Adjusting the criteria for viral contig confidence from ‘conservative’ to ‘eXtremely Conservative’ resulted in 37 841 HMM profiles in our efam-XC database. To assess the value of this resource, we integrated efam-XC into VirSorter viral discovery software to discover viruses from less-studied, ecologically distinct oxygen minimum zone (OMZ) marine habitats. This expanded database led to an increase in viruses recovered from every tested OMZ virome by ~24% on average (up to ~42%) and especially improved the recovery of often-missed shorter contigs (<5 kb). Additionally, to help elucidate lesser-known viral protein functions, we annotated the profiles using multiple databases from the DRAM pipeline and virion-associated metaproteomic data, which doubled the number of annotations obtainable by standard, single-database annotation approaches. Together, these marine resources (efam and efam-XC) are provided as searchable, compressed HMM databases that will be updated bi-annually to help maximize viral sequence discovery and study from any ecosystem.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗