Metatranscriptomic analysis of prokaryotic communities active in sulfur and arsenic cycling in Mono Lake, California, USA

Various microbial taxa couple arsenic transformation to nitrogen and carbon cycling in paddy soils

BACKGROUND

Arsenic (As) metabolism pathways and their coupling to nitrogen (N) and carbon (C) cycling contribute to elemental biogeochemical cycling. However, how whole-microbial communities respond to As stress and which taxa are the predominant As-transforming bacteria or archaea in situ remains unclear. Hence, by constructing and applying ROCker profiles to precisely detect and quantify As oxidation (aioA, arxA) and reduction (arrA, arsC1, arsC2) genes in short-read metagenomic and metatranscriptomic datasets, we investigated the dominant microbial communities involved in arsenite (As(III)) oxidation and arsenate (As(V)) reduction and revealed their potential pathways for coupling As with N and C in situ in rice paddies.

RESULTS

Five ROCker models were constructed to quantify the abundance and transcriptional activity of short-read sequences encoding As oxidation (aioA and arxA) and reduction (arrA, arsC1, arsC2) genes in paddy soils. Our results revealed that the sub-communities carrying the aioA and arsC2 genes were predominantly responsible for As(III) oxidation and As(V) reduction, respectively. Moreover, a newly identified As(III) oxidation gene, arxA, was detected in genomes assigned to various phyla and showed significantly increased transcriptional activity with increasing soil pH, indicating its important role in As(III) oxidation in alkaline soils. The significant correlation of the transcriptional activities of aioA with the narG and nirK denitrification genes, of arxA with the napA and nirS denitrification genes and of arrA/arsC2 with the pmoA and mcrA genes implied the coupling of As(III) oxidation with denitrification and As(V) reduction with methane oxidation. Various microbial taxa including Burkholderiales, Desulfatiglandales, and Hyphomicrobiales (formerly Rhizobiales) are involved in the coupling of As with N and C metabolism processes. Moreover, these correlated As and N/C genes often co-occur in the same genome and exhibit greater transcriptional activity in paddy soils with As contamination than in those without contamination.

CONCLUSIONS

Our results revealed the comprehensive detection and typing of short-read sequences associated with As oxidation and reduction genes via custom-built ROCker models, and shed light on the various microbial taxa involved in the coupling of As and N and C metabolism in situ in paddy soils. The contribution of the arxA sub-communities to the coupling of As(III) oxidation with nitrate reduction and the arsC sub-communities to the coupling of As(V) reduction with methane oxidation expands our knowledge of the interrelationships among As, N, and C cycling in paddy soils. Video Abstract.

Fate of arsenic in contaminated coastal soil induced by rising temperature and seawater intrusion

Temperature rising and seawater intrusion are expected to influence the hydrologic regime and redox conditions in coastal soil, and the fate and mechanisms of biogeochemical cycling of Arsenic (As) in the specific environment are poorly understood. This work was carried out in an anaerobic operating chamber by adding sulfate to simulate seawater intrusion under various temperature. Results demonstrated the microbial community diversity was influenced by temperature and the highest Shannon and lowest Simpson index were found at 28 °C. Firmicutes was the dominant bacteria, accounting for 81.16%-93.99%. Desulfosporosinus, with the proportion increasing with temperature, showed a significantly positive correlation with S2- for sulfate addition treatments. Actually, transformation of As was meditated by the concentration and valence of sulfur and iron in soil. The dissimilatory reduction of arsenic-bearing Fe oxides occurring in the initial stage, is suspected to be the primary driver of As release. Then, concentration of As declined in aqueous phase due to the reduction of sulfate, and the proportion of residual speciation of As in solid phase increased with temperature, ranging from 6.78% to 27.70%. The results displayed the reducing condition due to seawater intrusion and temperature change could regulate the release and sequestration of As in the coastal soil.

Sulfate-reducing bacteria unearthed: ecological functions of the diverse prokaryotic group in terrestrial environments

Sulfate-reducing prokaryotes (SRPs) are essential microorganisms that play crucial roles in various ecological processes. Even though SRPs have been studied for over a century, there are still gaps in our understanding of their biology. In the past two decades, a significant amount of data on SRP ecology has been accumulated. This review aims to consolidate that information, focusing on SRPs in soils, their relation to the rare biosphere, uncultured sulfate reducers, and their interactions with other organisms in terrestrial ecosystems. SRPs in soils form part of the rare biosphere and contribute to various processes as a low-density population. The data reveal a diverse range of sulfate-reducing taxa intricately involved in terrestrial carbon and sulfur cycles. While some taxa like Desulfitobacterium and Desulfosporosinus are well studied, others are more enigmatic. For example, members of the Acidobacteriota phylum appear to hold significant importance for the terrestrial sulfur cycle. Many aspects of SRP ecology remain mysterious, including sulfate reduction in different bacterial phyla, interactions with bacteria and fungi in soils, and the existence of soil sulfate-reducing archaea. Utilizing metagenomic, metatranscriptomic, and culture-dependent approaches will help uncover the diversity, functional potential, and adaptations of SRPs in the global environment.

Iron or sulfur respiration-an adaptive choice determining the fitness of a natronophilic bacterium Dethiobacter alkaliphilus in geochemically contrasting environments

Haloalkaliphilic microorganisms are double extremophiles functioning optimally at high salinity and pH. Their typical habitats are soda lakes, geologically ancient yet widespread ecosystems supposed to harbor relict microbial communities. We compared metabolic features and their determinants in two strains of the natronophilic species Dethiobacter alkaliphilus, the only cultured representative of the class "Dethiobacteria" (Bacillota). The strains of D. alkaliphilus were previously isolated from geographically remote Mongolian and Kenyan soda lakes. The type strain AHT1^T was described as a facultative chemolithoautotrophic sulfidogen reducing or disproportionating sulfur or thiosulfate, while strain Z-1002 was isolated as a chemolithoautotrophic iron reducer. Here, we uncovered the iron reducing ability of strain AHT1^T and the ability of strain Z-1002 for thiosulfate reduction and anaerobic Fe(II) oxidation. Key catabolic processes sustaining the growth of both D. alkaliphilus strains appeared to fit the geochemical settings of two contrasting natural alkaline environments, sulfur-enriched soda lakes and iron-enriched serpentinites. This hypothesis was supported by a meta-analysis of Dethiobacterial genomes and by the enrichment of a novel phylotype from a subsurface alkaline aquifer under Fe(III)-reducing conditions. Genome analysis revealed multiheme c-type cytochromes to be the most probable determinants of iron and sulfur redox transformations in D. alkaliphilus. Phylogeny reconstruction showed that all the respiratory processes in this organism are likely provided by evolutionarily related early forms of unconventional octaheme tetrathionate and sulfite reductases and their structural analogs, OmhA/OcwA Fe(III)-reductases. Several phylogenetically related determinants of anaerobic Fe(II) oxidation were identified in the Z-1002 genome, and the oxidation process was experimentally demonstrated. Proteomic profiling revealed two distinct sets of multiheme cytochromes upregulated in iron(III)- or thiosulfate-respiring cells and the cytochromes peculiar for Fe(II) oxidizing cells. We suggest that maintaining high variation in multiheme cytochromes is an effective adaptive strategy to occupy geochemically contrasting alkaline environments. We propose that sulfur-enriched soda lakes could be secondary habitats for D. alkaliphilus compared to Fe-rich serpentinites, and that the ongoing evolution of Dethiobacterales could retrace the evolutionary path that may have occurred in prokaryotes at a turning point in the biosphere's history, when the intensification of the sulfur cycle outweighed the global significance of the iron cycle.

Chemical Links Between Redox Conditions and Estimated Community Proteomes from 16S rRNA and Reference Protein Sequences

Environmental influences on community structure are often assessed through multivariate analyses in order to relate microbial abundances to separately measured physicochemical variables. However, genes and proteins are themselves chemical entities; in combination with genome databases, differences in microbial abundances directly encode for chemical variability. We predicted that the carbon oxidation state of estimated community proteomes, obtained by combining taxonomic abundances from published 16S rRNA gene sequencing datasets with reference microbial proteomes from the NCBI Reference Sequence (RefSeq) database, would reflect environmental oxidation-reduction conditions. Analysis of multiple datasets confirms the geobiochemical predictions for environmental redox gradients in hydrothermal systems, stratified lakes and marine environments, and shale gas wells. The geobiochemical signal is largest for the steep redox gradients associated with hydrothermal systems and between injected water and produced fluids from shale gas wells, demonstrating that microbial community composition can be a chemical proxy for environmental redox gradients. Although estimates of oxidation state from 16S amplicon and metagenomic sequences are correlated, the 16S-based estimates show stronger associations with redox gradients in some environments.

Effects of Mineral on Taxonomic and Functional Structures of Microbial Community in Tengchong Hot Springs via in-situ cultivation

Diverse mineralogical compositions occur in hot spring sediments, but the impact of minerals on the diversity and structure of microbial communities remains poorly elucidated. In this study, different mineral particles with various chemistries (i.e., hematite, biotite, K-feldspar, quartz, muscovite, aragonite, serpentine, olivine, barite, apatite, and pyrite) were incubated for ten days in two Tengchong hot springs, one alkaline (pH ~ 8.34) with a high temperature (~ 82.8 °C) (Gumingquan, short as GMQ) and one acidic (pH ~ 3.63) with a relatively low temperature (~ 43.3 °C) (Wenguangting, short as WGT), to determine the impacts of minerals on the microbial communities taxonomic and functional diversities. Results showed that the mineral-associated bacterial taxa differed from those of the bulk sediment samples in the two hot springs. The relative abundance of Proteobacteria, Euryarchaeota, and Acidobacteria increased in all minerals, indicating that these microorganisms are apt to colonize on solid surfaces. The α-diversity indices of the microbial communities on the mineral surfaces in the WGT were higher than those from the bulk sediment samples (p < 0.05), which may be caused by the stochastically adhering process on the mineral surface during 10-day incubation, different from the microbial community in sediment which has experienced long-term environmental and ecological screening. Chemoheterotrophy increased with minerals incubation, which was high in most cultured minerals (the relative contents were 5.8 - 21.4%). Most notably, the sulfate respiration bacteria (mainly related to Desulfobulbaceae and Syntrophaceae) associated with aragonite in the acidic hot spring significantly differed from other minerals, possibly due to the pH buffering effect of aragonite providing more favorable conditions for their survival and proliferation. By comparison, aragonite cultured in the alkaline hot spring highly enriched denitrifying bacteria and may have promoted the nitrogen cycle within the system. Collectively, we speculated that diverse microbes stochastically adhered on the surface of minerals in the water flows, and the physicochemical properties of minerals drove the enrichment of certain microbial communities and functional groups during the short-term incubation. Taken together, these findings thereby provide novel insights into mechanisms of community assembly and element cycling in the terrestrial hydrothermal system associated with hot springs.

Different sulfide to arsenic ratios driving arsenic speciation and microbial community interactions in two alkaline hot springs

Arsenic (As) is ubiquitous in geothermal fluids, which threatens both water supply safety and local ecology. The co-occurrence of sulfur (S) and As increases the complexity of As migration and transformation in hot springs. Microorganisms play important roles in As-S transformation processes. In the present study, two Tibetan alkaline hot springs (designated Gulu [GL] and Daba [DB]) with different total As concentrations (0.88 mg/L and 12.42 mg/L, respectively) and different sulfide/As ratios (3.97 and 0.008, respectively) were selected for investigating interactions between As-S geochemistry and microbial communities along the outflow channels. The results showed that As-S transformation processes were similar, although concentrations and percentages of As and S species differed between the two hot springs. Thioarsenates were detected at the vents of the hot springs (18% and 0.32%, respectively), and were desulfurized to arsenite along the drainage channel. Arsenite was finally oxidized to arsenate (532 μg/L and 12,700 μg/L, respectively). Monothioarsenate, total As, and sulfate were the key factors shaping the changes in microbial communities with geochemical gradients. The relative abundances of sulfur reduction genes (dsrAB) and arsenate reduction genes (arsC) were higher in upstream portions of GL explaining high thiolation. Arsenite oxidation genes (aoxAB) were relatively abundant in downstream parts of GL and at the vent of DB explaining low thiolation. Sulfur oxidation genes (soxABXYZ) were abundant in GL and DB. Putative sulfate-reducing bacteria (SRB), such as Desulfuromusa and Clostridium, might be involved in forming thioarsenates by producing reduced S for chemical reactions with arsenite. Sulfur-oxidizing bacteria (SOB), such as Elioraea, Pseudoxanthomonas and Pseudomonas, and arsenite-oxidizing bacteria (AsOB) such as Thermus, Sulfurihydrogenibium and Hydrogenophaga, may be responsible for the oxidation of As-bound S, thereby desulfurizing thioarsenates, forming arsenite and, by further abiotic or microbial oxidation, arsenate. This study improves our understanding of As and S biogeochemistry in hot springs.

Genome-Resolved Metagenomics and Metatranscriptomics Reveal that Aquificae Dominates Arsenate Reduction in Tengchong Geothermal Springs

Elevated arsenic (As) is common in geothermal springs, shaping the evolution of As metabolism genes and As transforming microbes. Herein, genome-level microbial metabolisms and As cycling strategies in Tengchong geothermal springs were demonstrated for the first time based on metagenomic and metatranscriptomic analyses. Sulfur cycling was dominated by Aquificae oxidizing thiosulfate via the sox system, fueling the respiration and carbon dioxide fixation processes. Arsenate reduction via arsC [488.63 ± 271.60 transcripts per million (TPM)] and arsenite efflux via arsB (442.98 ± 284.81 TPM) were the primary detoxification pathway, with most genes and transcripts contributed by the members in phylum Aquificae. A complete arsenotrophic cycle was also transcriptionally active as evidenced by the detection of aioA transcripts and arrA transcript reads mapped onto metagenome-assembled genomes (MAGs) affiliated with Crenarchaeota. MAGs affiliated with Aquificae had great potential of reducing arsenate via arsC and fixing nitrogen and carbon dioxide via nifDHK and reductive tricarboxylic acid (rTCA) cycle, respectively. Aquificae's arsenate reduction potential via arsC was observed for the first time at the transcriptional level. This study expands the diversity of the arsC-based arsenate-reducing community and highlights the importance of Aquificae to As biogeochemistry.

Diversity and biogenesis contribution of sulfate-reducing bacteria in arsenic-contaminated soils from realgar deposits

Microbial sulfate reduction, a vital mechanism for microorganisms living in anaerobic, sulfate-rich environments, is an essential aspect of the sulfur biogeochemical cycle. However, there has been no detailed investigation of the diversity and biogenesis contribution of sulfate-reducing bacteria in arsenic-contaminated soils from realgar deposits. To elucidate this issue, soil samples from representative abandoned realgar deposits were collected. Microcosm assays illustrated that all three samples (2-1, 2-2, and 2-3) displayed efficient sulfate and As(V)-respiring activities. Furthermore, a total of 28 novel sequence variants of dissimilatory sulfite reductase genes and 2 new families of dsrAB genes were successfully identified. A novel dissimilatory sulfate-reducing bacterium, Desulfotomaculum sp. JL1, was also isolated from soils, and can efficiently respiratory reduce As(V) and sulfate in 4 and 5 days, respectively. JL1 can promote the generation of yellow precipitates in the presence of multiple electron acceptors (both contain sulfate and As(V) in the cultures), which indicated the biogenesis contribution of sulfate-reducing bacteria to the realgar mine. Moreover, this area had unique microbial communities; the most abundant populations belonged to the phyla Proteobacteria, Chloroflexi, and Acidobacteriota, which were attributed to the unique geochemistry characteristics, such as total organic carbon, total As, NO₃^-, and SO₄^2-. The results of this study provide new insight into the diversity and biogenesis contributions of sulfate-reducing bacteria in arsenic-contaminated soils from realgar deposits.

A unique microbiome in a highly polluted and alkalic lake in a seasonally frozen area

Highly polluted waters profoundly promoted microbial activities and vice versa. Although microbial community structures and bioprocesses in polluted environments have been fully investigated, they are rarely uncovered in abandoned and highly polluted aquatic environment, especially in a seasonally frozen area. East Lake had been polluted by surrounding paper mills and dairy plants from the 1960s to the early 2000s. Under low biodegradability (BOD₅/COD ratio<0.2) and alkalic (pH > 9) conditions, a unique microbiome was discovered in East lake. Proteobacteria was the largest taxonomic group in the microbial community, covering almost half of the top-100 genera. Among them, seven genera are sulfate-reducing bacteria, including Desulfuromusa, Desulfuromonas, Desulfobulbus, Desulfocapsa, Desulfurivibrio, Desulfatiglans, and Desulfomicrobium. Functional analysis revealed abundant predicted functional genes for the respiration of sulfur compounds and sulfate respiration. Great vertical variations were found to both microbial community structures and predicted functions. This work provides unique evidence for future microbiome studies of nutrient-rich, alkalic, and seasonally frozen water habitats.

Environmental geochemistry of thioantimony: formation, structure and transformation as compared with thioarsenic

Antimony (Sb), a redox-sensitive toxic element, has received global attention due to the increased awareness of its rich geochemistry. The past two decades have witnessed the explosive development in geochemistry of oxyanionic Sb(OH)₃ and Sb(OH)₆^-. Emerging thioantimony species (Sb-S) have recently been detected, which actually dominate the Sb mobility in sulfate-reducing environments. However, the instability and complexity of Sb-S present the most pressing challenges. To overcome these barriers, it is urgent to summarize the existing research on the environmental geochemistry of Sb-S. Since Sb-S is an analogous species to thioarsenic (As-S), a comparison between Sb-S and As-S will provide insightful information. Therefore, this review presents a way of comparing environmental geochemistry between Sb-S and As-S. Here, we summarize the formation and transformation of Sb-S and As-S, their chemical structures and analytical methods. Then, the challenges and perspectives are discussed. Finally, the important scientific questions that need to be addressed are also proposed.

Sargassum Differentially Shapes the Microbiota Composition and Diversity at Coastal Tide Sites and Inland Storage Sites on Caribbean Islands

Rafts of drifting pelagic Sargassum that are circulating across the Atlantic Ocean are complex ecosystems composed of a large number of associated species. Upon massive stranding, they lead to various socio-environmental issues including the inflow of contaminants and human health concerns. In this study, we used metabarcoding approaches to examine the differences in both the eukaryotic- and prokaryotic-associated communities from Sargassum present in two islands of the Lesser Antilles, namely Guadeloupe and Martinique. We detected significant differences in microbial community structure and composition between landing Sargassum, the surrounding seawater, and Sargassum from inland storage sites. In total we identified 22,214 prokaryotic and 17,679 eukaryotic OTUs. Among them, functional prediction analyses revealed a number of prokaryotes that might contribute to organic matter decomposition, nitrogen cycling and gas production, including sulfate-reducing bacteria at coastal landing sites, and methanogenic archaea at inland storage sites. We also found that Metazoan was the most abundant group in Sargassum samples, with nematode clades that presented exclusive or specific richness and abundance patterns depending on their Sargassum substrate. Together, these molecular inventories of the micro- and meiofauna communities provide baseline information for further characterization of trophic interactions, algal organic matter decomposition and nutrient transfers at coastal and inland storage sites.

Highly integrated adaptive mechanisms in Spiribacter halalkaliphilus, a bacterium abundant in Chinese soda-saline lakes

Soda-saline lakes are polyextreme environments inhabited by many haloalkaliphiles, including one of the most abundant Spiribacter species. However, its mechanisms of adaptation are not ecophysiologically characterized. Based on a large-scale cultivation strategy, we obtained a representative isolate of this Spiribacter species whose relative abundance was the highest (up to 15.63%) in a wide range of salinities in the soda-saline lakes in Inner Mongolia, China. This species is a chemoorganoheterotrophic haloalkaliphile. It has a small and streamlined genome and utilizes a wide variety of compatible solutes to resist osmotic pressure and multiple monovalent cation/proton antiporters for pH homeostasis. In addition to growth enhancement by light under microaerobic conditions, cell growth, organic substrate consumption and polyhydroxybutyrate biosynthesis were also improved by inorganic sulfide. Both quantitative RT-PCR and enzymatic assays verified that sulfide:quinone oxidoreductase was upregulated during this process. Metatranscriptomic analysis indicated that all genes related to environmental adaptation were transcribed in natural environments. Overall, this study has identified a novel abundant haloalkaliphile with multiple and highly integrated adaptive strategies and found that inorganic sulfide was able to improve the adaptation of a heterotroph to polyextreme environments.

A critical assessment on the short-term response of microbial relative composition in a mine tailings soil amended with biochar and manure compost

Phytomanagement of tailings requires the use of soil conditioners to favour plant establishment, but their benefits on soil microbial composition need to be assessed. The goal of this work was to evaluate the effect of two organic amendments, manure compost and biochar, on soil bacterial and fungal composition at metallic mine tailings. The addition of compost caused stronger effects in most of soil parameters and microbial composition than biochar, especially at the initial stage of the experiment. However, the higher dependence on labile organic carbon for some bacterial groups at the treatments containing compost determined their decay along time (Flavobacteriales, Sphingobacteriales) and the appearance of other taxa more dependent on recalcitrant organic matter (Xanthomonadales, Myxococcales). Biochar favoured bacterial decomposers (Actinomycetales) specialised in high lignin and other recalcitrant carbon compounds. Unlike bacteria, only a few fungal orders increased their relative abundances in the treatments containing compost (Sordariales and Microascales) while the rest showed a decrease or remained unaltered. The mix biochar-compost may result the best option to support a more diverse microbial population in terms of soil functionality that is able to decompose both labile and recalcitrant carbon compounds. This may favour the resilience of the system against environmental stressors.

A novel biofilm bioreactor derived from a consortium of acidophilic arsenite-oxidizing bacteria for the cleaning up of arsenite from acid mine drainage

Arsenite (As(III)) was considered to be of great concern in acid mine drainage (AMD). A promising approach for cleaning up of arsenite from AMD is microbial oxidation of As(III) followed by adsorptions. However, there is virtually no research about the acidophilic bioreactor for As(III) oxidation so far. In this study, we formed a new biofilm bioreactor with a consortium of acidophilic As(III) oxidation bacteria. It is totally chemoautotrophic, with no need to add any carbon or other materials during the operations. It works well under pH 3.0-4.0, capable of oxidizing 1.0-20.0 mg/L As(III) in 3.0-4.5 h, respectively. A continuous operation of the bioreactor suggests that it is very stable and sustainable. Functional gene detection indicated that the biofilms possessed a unique diversity of As(III) oxidase genes. Taken together, this acidophilic bioreactor has great potential for industrial applications in the cleaning up of As(III) from AMD solution.

Microbial succession and dynamics in meromictic Mono Lake, California

Mono Lake is a closed-basin, hypersaline, alkaline lake located in Eastern Sierra Nevada, California, that is dominated by microbial life. This unique ecosystem offers a natural laboratory for probing microbial community responses to environmental change. In 2017, a heavy snowpack and subsequent runoff led Mono Lake to transition from annually mixed (monomictic) to indefinitely stratified (meromictic). We followed microbial succession during this limnological shift, establishing a two-year (2017-2018) water-column time series of geochemical and microbiological data. Following meromictic conditions, anoxia persisted below the chemocline and reduced compounds such as sulfide and ammonium increased in concentration from near 0 to ~400 and ~150 µM, respectively, throughout 2018. We observed significant microbial succession, with trends varying by water depth. In the epilimnion (above the chemocline), aerobic heterotrophs were displaced by phototrophic genera when a large bloom of cyanobacteria appeared in fall 2018. Bacteria in the hypolimnion (below the chemocline) had a delayed, but systematic, response reflecting colonization by sediment "seed bank" communities. Phototrophic sulfide-oxidizing bacteria appeared first in summer 2017, followed by microbes associated with anaerobic fermentation in spring 2018, and eventually sulfate-reducing taxa by fall 2018. This slow shift indicated that multi-year meromixis was required to establish a sulfate-reducing community in Mono Lake, although sulfide oxidizers thrive throughout mixing regimes. The abundant green alga Picocystis remained the dominant primary producer during the meromixis event, abundant throughout the water column including in the hypolimnion despite the absence of light and prevalence of sulfide. Our study adds to the growing literature describing microbial resistance and resilience during lake mixing events related to climatic events and environmental change.

Microbially-driven sulfur cycling microbial communities in different mangrove sediments

Microbially-driven sulfur cycling is a vital biogeochemical process in the sulfur-rich mangrove ecosystem. It is critical to evaluate the potential impact of sulfur transformation in mangrove ecosystems. To reveal the diversity, composition, and structure of sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) and underlying mechanisms, we analyzed the physicochemical properties and sediment microbial communities from an introduced mangrove species (Sonneratia apetala), a native mangrove species (Kandelia obovata) and the mudflat in Hanjiang River Estuary in Guangdong (23.27°N, 116.52°E), China. The results indicated that SOB was dominated by autotrophic Thiohalophilus and chemoautotrophy Chromatium in S. apetala and K. obovata, respectively, while Desulfatibacillum was the dominant genus of SRB in K. obovata sediments. Also, the redundancy analysis indicated that temperature, redox potential (ORP), and SO₄^2- were the significant factors influencing the sulfur cycling microbial communities with elemental sulfur (ES) as the key factor driver for SOB and total carbon (TC) for SRB in mangrove sediments. Additionally, the morphological transformation of ES, acid volatile sulfide (AVS) and SO₄^2- explained the variation of sulfur cycling microbial communities under sulfur-rich conditions, and we found mangrove species-specific dominant Thiohalobacter, Chromatium and Desulfatibacillum, which could well use ES and SO₄^2-, thus promoting the sulfur cycling in mangrove sediments. Meanwhile, the change of nutrient substances (TN, TC) explained why SOB were more susceptible to environmental changes than SRB. Sulfate reducing bacteria produces sulfide in anoxic sediments at depth that then migrate upward, toward fewer reducing conditions, where it's oxidized by sulfur oxidizing bacteria. This study indicates the high ability of SOB and SRB in ES, SO₄^2-_,S₂^- and S^2- generation and transformation in sulfur-rich mangrove ecosystems, and provides novel insights into sulfur cycling in other wetland ecosystems from a microbial perspective.

Next generation sequencing approaches to evaluate water and wastewater quality

The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies can provide holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop a new assay for each target organism or gene. However, several barriers have hampered wide-scale adoption of NGS by the water industry, including cost, need for specialized expertise and equipment, challenges with data analysis and interpretation, lack of standardized methods, and the rapid pace of development of new technologies. In this critical review, we provide an overview of the current state of the science of NGS technologies as they apply to water, wastewater, and recycled water. In addition, a systematic literature review was conducted in which we identified over 600 peer-reviewed journal articles on this topic and summarized their contributions to six key areas relevant to the water and wastewater fields: taxonomic classification and pathogen detection, functional and catabolic gene characterization, antimicrobial resistance (AMR) profiling, bacterial toxicity characterization, Cyanobacteria and harmful algal bloom identification, and virus characterization. For each application, we have presented key trends, noteworthy advancements, and proposed future directions. Finally, key needs to advance NGS technologies for broader application in water and wastewater fields are assessed.

Influence of Temperature and Sulfate Concentration on the Sulfate/Sulfite Reduction Prokaryotic Communities in the Tibetan Hot Springs

The distribution and diversity of sulfate/sulfite reduction prokaryotic (SRP) communities in hot springs from the Quzhuomu and Daggyai Geothermal Zone of Tibetan, China, was reported for the first time. In hot springs that are naturally hyperthermal and anoxic, the sulfur cycle is one of the most active cycles of the elements. The distribution of SRP in response to temperature is of great importance to the understanding of biogeochemical cycling of sulfur in geothermal features. Little is known about the SRP in geothermal zone. In this study, the diversity of SRP was investigated in the sediments from the Daggyai and Quzhuomu geothermal zone using PCR amplification, cloning and sequencing of the dissimilatory sulfite reductase beta subunit gene (dsrB). The abundance of dsrB and 16S rRNA genes, were determined by quantitative polymerase chain reactions. In addition, correlations of the SRP assemblages with environmental factors were analyzed by the aggregated boosted tree (ABT) statistical analysis. The results showed that SRP populations were diverse, but were mainly composed of Desulfobacterales, Desulfovibrionales, Syntrophobacterales, Clostridia and Nitrospirales, and large fraction (25%) of novel sequences have branched groups in the dsrB phylogenetic tree. In Quzhuomu geothermal zone, sulfate-rich hot springs are characterized by thick bacterial mats that are green or red and the SRP populations mainly appear at mid-temperature (50 °C to 70 °C). In low-sulfate hot springs in the Daggyai geothermal zone, although gray or pink streamers are widely formed at 60 °C to 80 °C, they prefer to inhabit in green mat at lower temperature (30 °C to 50 °C). With increasing temperature, the diversity of the dsrB gene at the OTU level (cutoff 97%) decreased, while its relative abundance increased. This result suggests that temperature played an important role in affecting dsrB gene distribution.

Succession of sulfur bacteria during decomposition of cyanobacterial bloom biomass in the shallow Lake Nanhu: An ex situ mesocosm study

Previous studies of the dynamics of sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) have focused on deep stratified lakes. The objective of this study is to present an in-depth investigation of the structure and dynamics of sulfur bacteria (including SRB and SOB) in the water column of shallow freshwater lakes. A cyanobacterial bloom biomass (CBB)-amended mesocosm experiment was conducted in this study, in which water was taken from a shallow eutrophic lake with sulfate levels near 40 mg L^-1. Illumina sequencing was used to investigate SRB and SOB species involved in CBB decomposition and the effects of the increases in sulfate input on the water column microbial community structure. The accumulation of dissolved sulfide (∑H₂S) produced by SRB during CBB decomposition stimulated the growth of SOB, and ∑H₂S was then oxidized back to sulfate by SOB in the water column. Chlorobaculum sequences (the main SOB species in the study) were significantly influenced by increases in sulfate input, with relative abundance increasing approximately four-fold in treatments amended with 40 mg L^-1 sulfate (referred to as 40S) when compared to the treatment without additional sulfate addition (referred to as CU). Additionally, an increase in SOB number was observed from day 26-37, concurrent with the decrease in SRB number, indicating the succession of sulfur bacteria. These findings suggest that biological sulfur oxidation and succession of sulfur bacteria occur in the water column during CBB decomposition in shallow freshwater ecosystems, and the increases in sulfate input stimulate microbial sulfur oxidation.

Methane, arsenic, selenium and the origins of the DMSO reductase family

Mononuclear molybdoenzymes of the dimethyl sulfoxide reductase (DMSOR) family catalyze a number of reactions essential to the carbon, nitrogen, sulfur, arsenic, and selenium biogeochemical cycles. These enzymes are also ancient, with many lineages likely predating the divergence of the last universal common ancestor into the Bacteria and Archaea domains. We have constructed rooted phylogenies for over 1,550 representatives of the DMSOR family using maximum likelihood methods to investigate the evolution of the arsenic biogeochemical cycle. The phylogenetic analysis provides compelling evidence that formylmethanofuran dehydrogenase B subunits, which catalyze the reduction of CO₂ to formate during hydrogenotrophic methanogenesis, constitutes the most ancient lineage. Our analysis also provides robust support for selenocysteine as the ancestral ligand for the Mo/W atom. Finally, we demonstrate that anaerobic arsenite oxidase and respiratory arsenate reductase catalytic subunits represent a more ancient lineage of DMSORs compared to aerobic arsenite oxidase catalytic subunits, which evolved from the assimilatory nitrate reductase lineage. This provides substantial support for an active arsenic biogeochemical cycle on the anoxic Archean Earth. Our work emphasizes that the use of chalcophilic elements as substrates as well as the Mo/W ligand in DMSORs has indelibly shaped the diversification of these enzymes through deep time.

Bacterial Communities and Functional Genes Stimulated During Anaerobic Arsenite Oxidation and Nitrate Reduction in a Paddy Soil

Microbial arsenite (As(III)) oxidation associated with nitrate (NO₃^-) reduction might be an important process in diminishing arsenic bioavailability and toxicity to rice when paddy soils are contaminated by arsenic. In a noncontaminated soil, however, the responses of bacterial communities and functional genes to As(III) under nitrate-reducing conditions are poorly understood. In this study, anaerobic paddy soil microcosms were established with As(III) and/or NO₃^- to investigate how the bacterial communities and their functional genes were stimulated during As(III) oxidation and nitrate reduction. Microbial oxidation of As(III) to As(V) was substantially accelerated by nitrate addition, while nitrate reduction was not affected by As(III) addition. Metagenomic analysis revealed that nitrate-reducing bacteria were principally affiliated with Pseudogulbenkiania, with narG, nirS, and norBC genes. Putative As(III)-oxidizing bacteria were dominated by an Azoarcus sp. with As(III) oxidase genes aioA and aioB detected in its draft genome, which also had complete sets of denitrification genes (mainly, napA, nirK, and nosZ). Quantitive PCR analysis confirmed that the abundance of Azoarcus spp., aioA, and nosZ genes was enhanced by As(III) addition. These findings suggest the importance of Azoarcus- and Pseudogulbenkiania-related spp., both of which showed various physio-ecological characteristics for arsenic and nitrogen biogeochemistry, in coupling As(III) oxidation and nitrate reduction in flooded paddy soil.

Coastal Ocean Metagenomes and Curated Metagenome-Assembled Genomes from Marsh Landing, Sapelo Island (Georgia, USA)

Microbes play a dominant role in the biogeochemistry of coastal waters, which receive organic matter from diverse sources. We present metagenomes and 45 metagenome-assembled genomes (MAGs) from Sapelo Island, Georgia, to further understand coastal microbial populations. Notably, four MAGs are archaea, with two Thaumarchaeota and two marine group II Euryarchaeota.

Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake

BACKGROUND

The planetary sulfur cycle is a complex web of chemical reactions that can be microbial-mediated or can occur spontaneously in the environment, depending on the temperature and pH. Inorganic sulfur compounds can serve as energy sources for specialized prokaryotes and are important substrates for microbial growth in general. Here, we investigate dissimilatory sulfur cycling in the brine and sediments of a southwestern Siberian soda lake characterized by an extremely high pH and salinity, combining meta-omics analyses of its uniquely adapted highly diverse prokaryote communities with biogeochemical profiling to identify key microbial players and expand our understanding of sulfur cycling under haloalkaline conditions.

RESULTS

Peak microbial activity was found in the top 4 cm of the sediments, a layer with a steep drop in oxygen concentration and redox potential. The majority of sulfur was present as sulfate or iron sulfide. Thiosulfate was readily oxidized by microbes in the presence of oxygen, but oxidation was partially inhibited by light. We obtained 1032 metagenome-assembled genomes, including novel population genomes of characterized colorless sulfur-oxidizing bacteria (SOB), anoxygenic purple sulfur bacteria, heterotrophic SOB, and highly active lithoautotrophic sulfate reducers. Surprisingly, we discovered the potential for nitrogen fixation in a new genus of colorless SOB, carbon fixation in a new species of phototrophic Gemmatimonadetes, and elemental sulfur/sulfite reduction in the "Candidatus Woesearchaeota." Polysulfide/thiosulfate and tetrathionate reductases were actively transcribed by various (facultative) anaerobes.

CONCLUSIONS

The recovery of over 200 genomes that encoded enzymes capable of catalyzing key reactions in the inorganic sulfur cycle indicates complete cycling between sulfate and sulfide at moderately hypersaline and extreme alkaline conditions. Our results suggest that more taxonomic groups are involved in sulfur dissimilation than previously assumed.

Transcriptomic Analysis of Two Thioalkalivibrio Species Under Arsenite Stress Revealed a Potential Candidate Gene for an Alternative Arsenite Oxidation Pathway

The genus Thioalkalivibrio includes haloalkaliphilic chemolithoautotrophic sulfur-oxidizing bacteria isolated from various soda lakes worldwide. Some of these lakes possess in addition to their extreme haloalkaline environment also other harsh conditions, to which Thioalkalivibrio needs to adapt. An example is arsenic in soda lakes in eastern California, which is found there in concentrations up to 3000 μM. Arsenic is a widespread element that can be an environmental issue, as it is highly toxic to most organisms. However, resistance mechanisms in the form of detoxification are widespread and some prokaryotes can even use arsenic as an energy source. We first screened the genomes of 76 Thioalkalivibrio strains for the presence of known arsenic oxidoreductases and found 15 putative ArxA (arsenite oxidase) and two putative ArrA (arsenate reductase). Subsequently, we studied the resistance to arsenite in detail in Thioalkalivibrio jannaschii ALM2^T, and Thioalkalivibrio thiocyanoxidans ARh2^T by comparative genomics and by growing them at different arsenite concentrations followed by arsenic species and transcriptomic analysis. Tv. jannaschii ALM2^T, which has been isolated from Mono Lake, an arsenic-rich soda lake, could resist up to 5 mM arsenite, whereas Tv. thiocyanoxidans ARh2^T, which was isolated from a Kenyan soda lake, could only grow up to 0.1 mM arsenite. Interestingly, both species oxidized arsenite to arsenate under aerobic conditions, although Tv. thiocyanoxidans ARh2^T does not contain any known arsenite oxidases, and in Tv. jannaschii ALM2^T, only arxB2 was clearly upregulated. However, we found the expression of a SoeABC-like gene, which we assume might have been involved in arsenite oxidation. Other arsenite stress responses for both strains were the upregulation of the vitamin B₁₂ synthesis pathway, which can be linked to antioxidant activity, and the up- and downregulation of different DsrE/F-like genes whose roles are still unclear. Moreover, Tv. jannaschii ALM2^T induced the ars gene operon and the Pst system, and Tv. thiocanoxidans ARh2^T upregulated the sox and apr genes as well as different heat shock proteins. Our findings for Thioalkalivibrio confirm previously observed adaptations to arsenic, but also provide new insights into the arsenic stress response and the connection between the arsenic and the sulfur cycle.

Metagenomic insights into the abundance and composition of resistance genes in aquatic environments: Influence of stratification and geography

A global survey was performed with 122 aquatic metagenomic DNA datasets (92 lake water and 30 seawater) obtained from the Sequence Read Archive (SRA). Antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) were derived from the dataset sequences via bioinformatic analysis. The relative abundances of ARGs and MRGs in lake samples were in the ranges ND (not detected)-1.34 × 10⁰ and 1.22 × 10^-3-1.98 × 10^-1 copies per 16S rRNA, which were higher than those in seawater samples. Among ARGs, multidrug resistance genes and bacitracin resistance genes had high relative abundances in both lake and sea water samples. Multi-metal resistance genes, mercury resistance genes and copper resistance genes had the greatest relative abundance for MRGs. No significant difference was found between epilimnion and hypolimnion in abundance or the Shannon diversity index for ARGs and MRGs. Principal coordinates analysis and permutational multivariate analysis of variance (PERMANOVA) test showed that stratification and geography had significant influence on the composition of ARGs and MRGs in lakes (p < 0.05, PERMANOVA). Coastal seawater samples had significantly greater relative abundance and a higher Shannon index for both ARGs and MRGs than deep ocean and Antarctic seawater samples (p < 0.05, Kruskal-Wallis one-way ANOVA), suggesting that human activity may exert more selective pressure on ARGs and MRGs in coastal areas than those in deep ocean and Antarctic seawater.

A global survey of arsenic-related genes in soil microbiomes

BACKGROUND

Environmental resistomes include transferable microbial genes. One important resistome component is resistance to arsenic, a ubiquitous and toxic metalloid that can have negative and chronic consequences for human and animal health. The distribution of arsenic resistance and metabolism genes in the environment is not well understood. However, microbial communities and their resistomes mediate key transformations of arsenic that are expected to impact both biogeochemistry and local toxicity.

RESULTS

We examined the phylogenetic diversity, genomic location (chromosome or plasmid), and biogeography of arsenic resistance and metabolism genes in 922 soil genomes and 38 metagenomes. To do so, we developed a bioinformatic toolkit that includes BLAST databases, hidden Markov models and resources for gene-targeted assembly of nine arsenic resistance and metabolism genes: acr3, aioA, arsB, arsC (grx), arsC (trx), arsD, arsM, arrA, and arxA. Though arsenic-related genes were common, they were not universally detected, contradicting the common conjecture that all organisms have them. From major clades of arsenic-related genes, we inferred their potential for horizontal and vertical transfer. Different types and proportions of genes were detected across soils, suggesting microbial community composition will, in part, determine local arsenic toxicity and biogeochemistry. While arsenic-related genes were globally distributed, particular sequence variants were highly endemic (e.g., acr3), suggesting dispersal limitation. The gene encoding arsenic methylase arsM was unexpectedly abundant in soil metagenomes (median 48%), suggesting that it plays a prominent role in global arsenic biogeochemistry.

CONCLUSIONS

Our analysis advances understanding of arsenic resistance, metabolism, and biogeochemistry, and our approach provides a roadmap for the ecological investigation of environmental resistomes.

Arsenite Oxidation by a Newly Isolated Betaproteobacterium Possessing arx Genes and Diversity of the arx Gene Cluster in Bacterial Genomes

Microbes play essential roles in arsenic transformation in the environment. Microbial arsenite oxidation is catalyzed by either of two distantly related arsenite oxidases, referred to as AIO and ARX. The arx genes encoding ARX and its regulatory proteins were originally defined in the genomes of gammaproteobacteria isolated from an alkaline soda lake. The arx gene cluster has been identified in a limited number of bacteria, predominantly in gammaproteobacteria isolated from lakes characterized by high pH and high salinity. In the present study, a novel arsenite-oxidizing betaproteobacterium, strain M52, was isolated from a hot spring microbial mat. The strain oxidized arsenite under both microaerophilic and nitrate-reducing conditions at nearly neutral pH. Genome analysis revealed that the strain possesses the arx gene cluster in its genome and lacks genes encoding AIO. Inspection of the bacterial genomes available in the GenBank database revealed that the presence of this gene cluster is restricted to genomes of Proteobacteria, mainly in the classes Gammaproteobacteria and Betaproteobacteria. In these genomes, the structure of the gene cluster was generally well-conserved, but genes for regulatory proteins were lacking in genomes of strains belonging to a specific lineage. Phylogenetic analysis suggested that ARX encoded in the genomes can be divided into three groups, and strain M52 belongs to a group specific for organisms living in low-salt environments. The ArxA protein encoded in the genome of strain M52 was characterized by the presence of a long insertion, which was specifically observed in the same group of ARX. In clone library analyses with a newly designed primer pair, a diverse ArxA sequence with a long insertion was detected in samples of lake water and hot spring microbial mat, characterized by low salinity and a nearly neutral pH. Among the isolated bacterial strains whose arsenite oxidation has been demonstrated, strain M52 is the first betaproteobacterium that possesses the arx genes, the first strain encoding ARX of the group specific for low-salt environments, and the first organism possessing the gene encoding ArxA with a long insertion.

Spatio-temporal dynamics of sulfur bacteria during oxic--anoxic regime shifts in a seasonally stratified lake

Sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria drive major transformations in the sulfur cycle, and play vital roles in oxic--anoxic transitions in lakes and coastal waters. However, information on the succession of these sulfur bacteria in seasonally stratified lakes using molecular biological techniques is scarce. Here, we used 16S rRNA gene amplicon sequencing to study the spatio-temporal dynamics of sulfur bacteria during oxic--anoxic regime shifts in Lake Vechten. Oxygen and sulfate were mixed throughout the water column in winter and early spring. Meanwhile, SRB, green sulfur bacteria (GSB), purple sulfur bacteria (PSB), and colorless sulfur bacteria (CSB) exclusively inhabited the sediment. After the water column stratified, oxygen and nitrate concentrations decreased in the hypolimnion and various SRB species expanded into the anoxic hypolimnion. Consequently, sulfate was reduced to sulfide, stimulating the growth of PSB and GSB in the metalimnion and hypolimnion during summer stratification. When hypoxia spread throughout the water column during fall turnover, SRB and GSB vanished from the water column, whereas CSB (mainly Arcobacter) and PSB (Lamprocystis) became dominant and oxidized the accumulated sulfide under micro-aerobic conditions. Our results support the view that, once ecosystems have become anoxic and sulfidic, a large oxygen influx is needed to overcome the anaerobic sulfur cycle and bring the ecosystems back into their oxic state.

Impacts of Human Activities on the Composition and Abundance of Sulfate-Reducing and Sulfur-Oxidizing Microorganisms in Polluted River Sediments

Water system degradation has a severe impact on daily life, especially in developing countries. However, microbial changes associated with this degradation, especially changes in microbes related to sulfur (S) cycling, are poorly understood. In this study, the abundance, structure, and diversity of sulfate-reducing microorganisms (SRM) and sulfur-oxidizing microorganisms (SOM) in the sediments from the Ziya River Basin, which is polluted by various human interventions (urban and agricultural activities), were investigated. Quantitative real-time PCR showed that the S cycling-related (SCR) genes (dsrB and soxB) were significantly elevated, reaching 2.60 × 10⁷ and 1.81 × 10⁸ copies per gram of dry sediment, respectively, in the region polluted by human urban activities (RU), and the ratio of dsrB to soxB abundance was significantly elevated in the region polluted by human agricultural activities (RA) compared with those in the protected wildlife reserve (RP), indicating that the mechanisms underlying water system degradation differ between RU and RA. Based on a 16S rRNA gene analysis, human interventions had substantial effects on microbial communities, particularly for microbes involved in S cycling. Some SCR genera (i.e., Desulfatiglans and Geothermobacter) were enriched in the sediments from both RA and RU, while others (i.e., Desulfofustis and Desulfonatronobacter) were only enriched in the sediments from RA. A redundancy analysis indicated that NH₄⁺-N and total organic carbon significantly influenced the abundance of SRM and SOM, and sulfate significantly influenced only the abundance of SRM. A network analysis showed high correlation between SCR microorganisms and other microbial groups for both RU and RA, including those involved in carbon and metal cycling. These findings indicated the different effects of different human interventions on the microbial community composition and water quality degradation.

Changes in Carbon Oxidation State of Metagenomes Along Geochemical Redox Gradients

There is widespread interest in how geochemistry affects the genomic makeup of microbial communities, but the possible impacts of oxidation-reduction (redox) conditions on the chemical composition of biomacromolecules remain largely unexplored. Here we document systematic changes in the carbon oxidation state, a metric derived from the chemical formulas of biomacromolecular sequences, using published metagenomic and metatranscriptomic datasets from 18 studies representing different marine and terrestrial environments. We find that the carbon oxidation states of DNA, as well as proteins inferred from coding sequences, follow geochemical redox gradients associated with mixing and cooling of hot spring fluids in Yellowstone National Park (USA) and submarine hydrothermal fluids. Thermodynamic calculations provide independent predictions for the environmental shaping of the gene and protein composition of microbial communities in these systems. On the other hand, the carbon oxidation state of DNA is negatively correlated with oxygen concentration in marine oxygen minimum zones. In this case, a thermodynamic model is not viable, but the low carbon oxidation state of DNA near the ocean surface reflects a low GC content, which can be attributed to genome reduction in organisms adapted to low-nutrient conditions. We also present evidence for a depth-dependent increase of oxidation state at the species level, which might be associated with alteration of DNA through horizontal gene transfer and/or selective degradation of relatively reduced (AT-rich) extracellular DNA by heterotrophic bacteria. Sediments exhibit even more complex behavior, where carbon oxidation state minimizes near the sulfate-methane transition zone and rises again at depth; markedly higher oxidation states are also associated with older freshwater-dominated sediments in the Baltic Sea that are enriched in iron oxides and have low organic carbon. This geobiochemical study of carbon oxidation state reveals a new aspect of environmental information in metagenomic sequences, and provides a reference frame for future studies that may use ancient DNA sequences as a paleoredox indicator.

Metabolic Capability and Phylogenetic Diversity of Mono Lake during a Bloom of the Eukaryotic Phototroph Picocystis sp. Strain ML

Algal blooms in lakes are often associated with anthropogenic eutrophication; however, they can occur without the human introduction of nutrients to a lake. A rare bloom of the alga Picocystis sp. strain ML occurred in the spring of 2016 at Mono Lake, a hyperalkaline lake in California, which was also at the apex of a multiyear-long drought. These conditions presented a unique sampling opportunity to investigate microbiological dynamics and potential metabolic function during an intense natural algal bloom. We conducted a comprehensive molecular analysis along a depth transect near the center of the lake from the surface to a depth of 25 m in June 2016. Across sampled depths, rRNA gene sequencing revealed that Picocystis-associated chloroplasts were found at 40 to 50% relative abundance, greater than values recorded previously. Despite high relative abundances of the photosynthetic oxygenic algal genus Picocystis, oxygen declined below detectable limits below a depth of 15 m, corresponding with an increase in microorganisms known to be anaerobic. In contrast to previously sampled years, both metagenomic and metatranscriptomic data suggested a depletion of anaerobic sulfate-reducing microorganisms throughout the lake's water column. Transcripts associated with photosystem I and II were expressed at both 2 m and 25 m, suggesting that limited oxygen production could occur at extremely low light levels at depth within the lake. Blooms of Picocystis appear to correspond with a loss of microbial activity such as sulfate reduction within Mono Lake, yet microorganisms may survive within the sediment to repopulate the lake water column as the bloom subsides.IMPORTANCE Mono Lake, California, provides a habitat to a unique ecological community that is heavily stressed due to recent human water diversions and a period of extended drought. To date, no baseline information exists from Mono Lake to understand how the microbial community responds to human-influenced drought or algal bloom or what metabolisms are lost in the water column as a consequence of such environmental pressures. While previously identified anaerobic members of the microbial community disappear from the water column during drought and bloom, sediment samples suggest that these microorganisms survive at the lake bottom or in the subsurface. Thus, the sediments may represent a type of seed bank that could restore the microbial community as a bloom subsides. Our work sheds light on the potential photosynthetic activity of the halotolerant alga Picocystis sp. strain ML and how the function and activity of the remainder of the microbial community responds during a bloom at Mono Lake.

Autotrophic microbial arsenotrophy in arsenic-rich soda lakes

A number of prokaryotes are capable of employing arsenic oxy-anions as either electron acceptors [arsenate; As(V)] or electron donors [arsenite; As(III)] to sustain arsenic-dependent growth ('arsenotrophy'). A subset of these microorganisms function as either chemoautotrophs or photoautotrophs, whereby they gain sufficient energy from their redox metabolism of arsenic to completely satisfy their carbon needs for growth by autotrophy, that is the fixation of inorganic carbon (e.g. HCO3-) into their biomass. Here we review what has been learned of these processes by investigations we have undertaken in three soda lakes of the western USA and from the physiological characterizations of the relevant bacteria, which include the critical genes involved, such as respiratory arsenate reductase (arrA) and the discovery of its arsenite-oxidizing counterpart (arxA). When possible, we refer to instances of similar process occurring in other, less extreme ecosystems and by microbes other than haloalkaliphiles.

Complete genome of Halomonas aestuarii Hb3, isolated from tidal flat

Halomonas aestuarii Hb3, a moderately halophilic bacterium belonging to the class Gammaproteobacteria, was isolated from a tidal flat. Herein, we report the complete genome sequence of its strain Hb3. Its size is estimated at 3.54Mbp with a mean G+C content of 67.9%. The genome includes 3238 open reading frames, 65 transfer RNAs, and four ribosomal RNA gene operons. Genes related to the degradation of monoaromatic compounds, detoxification of arsenic, and production of polymers were identified. These features indicate that this strain may be important for ecological and industrial application.

Composition and Activity of Microbial Communities along the Redox Gradient of an Alkaline, Hypersaline, Lake

We compared the composition of microbial communities obtained by sequencing 16S rRNA gene amplicons with taxonomy derived from metatranscriptomes from the same samples. Samples were collected from alkaline, hypersaline Mono Lake, California, USA at five depths that captured the major redox zones of the lake during the onset of meromixis. The prokaryotic community was dominated by bacteria from the phyla Proteobacteria, Firmicutes, and Bacteroidetes, while the picoeukaryotic chlorophyte Picocystis dominated the eukaryotes. Most (80%) of the abundant (>1% relative abundance) OTUs recovered as amplicons of 16S rRNA genes have been reported in previous surveys, indicating that Mono Lake's microbial community has remained stable over 12 years that have included periods of regular, annual overturn interspersed by episodes of prolonged meromixis that result in extremely reducing conditions in bottom water. Metatranscriptomic sequences binned predominately to the Gammaproteobacteria genera Thioalkalivibrio (4–13%) and Thioalkalimicrobium (0–14%); and to the Firmicutes genera Dethiobacter (0–5%) and Clostridium (1–4%), which were also abundant in the 16S rRNA gene amplicon libraries. This study provides insight into the taxonomic affiliations of transcriptionally active communities of the lake's water column under different redox conditions.

Arsenite as an Electron Donor for Anoxygenic Photosynthesis: Description of Three Strains of Ectothiorhodospira from Mono Lake, California and Big Soda Lake, Nevada

Three novel strains of photosynthetic bacteria from the family Ectothiorhodospiraceae were isolated from soda lakes of the Great Basin Desert, USA by employing arsenite (As(III)) as the sole electron donor in the enrichment/isolation process. Strain PHS-1 was previously isolated from a hot spring in Mono Lake, while strain MLW-1 was obtained from Mono Lake sediment, and strain BSL-9 was isolated from Big Soda Lake. Strains PHS-1, MLW-1, and BSL-9 were all capable of As(III)-dependent growth via anoxygenic photosynthesis and contained homologs of arxA, but displayed different phenotypes. Comparisons were made with three related species: Ectothiorhodospira shaposhnikovii DSM 2111, Ectothiorhodospira shaposhnikovii DSM 243T, and Halorhodospira halophila DSM 244. All three type cultures oxidized arsenite to arsenate but did not grow with As(III) as the sole electron donor. DNA-DNA hybridization indicated that strain PHS-1 belongs to the same species as Ect. shaposhnikovii DSM 2111 (81.1% sequence similarity), distinct from Ect. shaposhnikovii DSM 243T (58.1% sequence similarity). These results suggest that the capacity for light-driven As(III) oxidation is a common phenomenon among purple photosynthetic bacteria in soda lakes. However, the use of As(III) as a sole electron donor to sustain growth via anoxygenic photosynthesis is confined to novel isolates that were screened for by this selective cultivation criterion.