Activity and community structures of sulfate-reducing microorganisms in polar, temperate and tropical marine sediments

Study of Stratification of Prokaryotic Microbial Communities in Sediments of Velikaya Salma Strait and Kandalaksha Bay, the White Sea

The stratification of prokaryotic microbial communities in shallow and deep-water sediments was investigated in two locations of the White Sea: Velikaya Salma Strait and the deep-water part of Kandalaksha Bay. Taxonomic diversity was analyzed using 16S rRNA gene-based profiling across horizontal sediment layers down to a depth of 50 cm. A total of 55 samples were collected from 15 stations: 43 from 11 shallow-water stations (including 4 in "gas cap" areas) at 2-50 cm depths and 12 from 4 deep-water stations at 2-30 cm. CH4 concentrations were measured for all stations, while total organic carbon (TOC) content was determined for selected sites. In Velikaya Salma Strait, the upper sediment layers were dominated by microorganisms involved in labile organic matter degradation and sulfate reduction, including Woeseia, Sandaracinaceae, Actinomarinales, SEEP-SRB1, and Sva0081. Deeper layers exhibited a shift toward taxa capable of degrading complex and recalcitrant substrates, such as Desulfatiglans, Hyphomicrobiaceae, and Mycobacterium, alongside uncultured microorganisms belonging to groups like SG8-4, WCHB1-81, Aerophobales, S085, JS1, and Anaerolineaceae. Notably, JS1 made up to half of the microorganisms in deeper layers, highlighting their ecological significance. In "gas cap"-associated sediments no pronounced stratification was observed with more homogeneous microbial community composition across all horizons. Similarly, in the deep-water part of Kandalaksha Bay, the microbial community showed minimal vertical differentiation. The dominant taxa in deep-water sediments included SEEP-SRB1, Sva0081, Sandaracinaceae, Anaerolineaceae, Woeseia, and PHOS-HE36. This study highlights the variability in microbial community structure across sediment depths and environmental conditions in Kandalaksha Bay.

Assessing spatial and temporal patterns of benthic bacterial communities in response to different sediment conditions

Benthic bacterial communities are sensitive to habitat condition and present a fast response to environmental stressors, which makes them powerful ecological indicators of estuarine environments. The aim of this work is to study the spatial-temporal patterns of benthic bacterial communities in response to contrasting environmental conditions and assess their potential as ecological indicators of estuarine sediments. We characterized the diversity of bacterial communities in three contrasting sites on Sado Estuary (SW Coast, Portugal) and 4 sampling occasions, using 16S metagenomic approach. Based on previous studies, we hypothesized that diversity patterns of bacterial communities will be distinct between sites and across sampling occasions. Bacterial communities were more influenced by each site conditions than by temporal variations in the sediments. The main drivers of bacterial distribution were sediments' composition, organic contents, and hydrodynamic activity. This work provided an important baseline dataset from Sado estuary to explore bacterial networks concerning benthic ecosystem functioning.

Methane emission fluxes and associated microbial community characteristics in a temperate seagrass meadow

Seagrass meadows are acknowledged as blue carbon ecosystems, yet they are also ideal habitats for methane (CH4) release, offsetting their ability to mitigate climate change. The global CH4 fluxes in seagrass meadows remain highly uncertain due to regional and species biases, and the microbial mechanisms driving methane release are poorly understood. Here, we investigated CH4 air-sea fluxes, sediment CH4 emission potential and microbes involved in CH4 release using geochemical techniques combined with qPCR and Illumina sequencing in a temperate Zostera japonica and Zostera marina mixed meadow. The CH4 air-sea fluxes fluctuated from -0.42 to 11.42 μmol·m-2·d-1, showing a strong seasonal variation. CH4 emission potential was significantly higher in seagrass vegetated sediments (10.34 ± 2.72 nmol·g-1·d-1) than in the adjacent bare sediments (1.55 ± 1.15 nmol·g-1·d-1), primarily attributed to variations in sediment organic matter content. Diverse methanogens occurred in the seagrass meadow, with Methanolobus dominating in seagrass sediments, while Methanococcoides, Methanosarcina, and Methanoculleus being prevalent in bare sediments. Meanwhile, a variety of methylotrophic groups were detected, including aerobic Gammaproteobacteria, anaerobic Desulfobacterota and Methylomirabilota, as well as archaea Candidatus Methanoperedens. The co-occurrence of these functional groups implied the presence of complex CH4 production and oxidation pathways, which regulated the CH4 budget in the seagrass ecosystems. Taken together, our findings enhance the comprehension of the methane emission process and driving mechanism in seagrass ecosystems.

Microbial communities and their role in enhancing hemp fiber quality through field retting

The current development of industrial hemp "Cannabis Sativa L." fibers for technical textiles and industrial applications requires high-quality fibers with homogeneous properties. However, several factors have been reported to influence the fibers' intrinsic properties, including a post-harvest process known as retting. This process plays a crucial role in facilitating the mechanical extraction of fibers from hemp stems. Retting involves the degradation of the amorphous components surrounding the fiber bundles enabling their decohesion from stems. Microorganisms play a central role in mediating this bioprocess. During retting, they colonize the stems' surface. Therefore, the biochemical components of plant cell wall, acting as natural binding between fibers, undergo a breakdown through the production of microbial enzymes. Although its critical role, farmers often rely on empirical retting practices, and considering various biotic and abiotic factors, resulting in fibers with heterogenous properties. These factors limit the industrial applications of hemp fibers due to their inconsistent properties. Thus, the purpose of this review is to enhance our comprehension of how retting influences the dynamics of microbial communities and, consequently, the evolution of the biochemical properties of hemp stems throughout this process. Better understanding of retting is crucial for effective process management, leading to high-value fibers. KEY POINTS: • Retting enables degradation of cell wall components, controlling fiber properties. • Microbial enzymatic activity is crucial for successful decohesion of fiber bundles. • Understanding retting mechanisms is essential for consistent fiber production.

Spatial distribution of cable bacteria in nationwide organic-matter-polluted urban rivers in China

An overload of labile organic matter triggers the water blackening and odorization in urban rivers, leading to a unique microbiome driving biogeochemical cycles in these anoxic habitats. Among the key players in these environments, cable bacteria interfere directly with C/N/S/O cycling, and are closely associated with phylogenetically diverse microorganisms in anoxic sediment as an electron conduit to mediate long-distance electron transport from deep-anoxic-layer sulfide to oxic-layer oxygen. Despite their hypothesized importance in black-odorous urban rivers, the spatial distribution patterns and roles of cable bacteria in large-scale polluted urban rivers remain inadequately understood. This study examined the diversity and spatial distribution pattern of cable bacteria in sediment samples from 186 black-odorous urban rivers across China. Results revealed the co-existence of two well-characterized cable bacteria (i.e., Candidatus Electrothrix and Candidatus Electronema), with Candidatus Electrothrix exhibiting a comparatively wider distribution in the polluted urban rivers. Concentrations of DOC, SS, sulfate, nitrate, and heavy metals (e.g., Ni and Cr) were correlated with the cable bacteria diversity, indicating their essential role in biogeochemical cycles. The activation energy of cable bacteria was 0.624 eV, close to the canonical 0.65 eV. Furthermore, cable bacteria were identified as key connectors and module hubs, closely associated with denitrifiers, sulfate-reducing bacteria, methanogens and alkane degraders, highlighting their role as keystone functional lineages in the contaminated urban rivers. Our study provided the first large-scale and comprehensive insight into the cable bacteria diversity, spatial distribution, and their essential function as keystone species in organic-matter-polluted urban rivers.

Electron Transfer in the Biogeochemical Sulfur Cycle

Microorganisms are key players in the global biogeochemical sulfur cycle. Among them, some have garnered particular attention due to their electrical activity and ability to perform extracellular electron transfer. A growing body of research has highlighted their extensive phylogenetic and metabolic diversity, revealing their crucial roles in ecological processes. In this review, we delve into the electron transfer process between sulfate-reducing bacteria and anaerobic alkane-oxidizing archaea, which facilitates growth within syntrophic communities. Furthermore, we review the phenomenon of long-distance electron transfer and potential extracellular electron transfer in multicellular filamentous sulfur-oxidizing bacteria. These bacteria, with their vast application prospects and ecological significance, play a pivotal role in various ecological processes. Subsequently, we discuss the important role of the pili/cytochrome for electron transfer and presented cutting-edge approaches for exploring and studying electroactive microorganisms. This review provides a comprehensive overview of electroactive microorganisms participating in the biogeochemical sulfur cycle. By examining their electron transfer mechanisms, and the potential ecological and applied implications, we offer novel insights into microbial sulfur metabolism, thereby advancing applications in the development of sustainable bioelectronics materials and bioremediation technologies.

Distribution of mercury in modern bottom sediments of the Beaufort Sea in relation to the processes of early diagenesis: Microbiological aspect

This study investigated the contents of total mercury (THg), trace metals, and CH4 and determined the signature microbes involved in various biogeochemical processes in the sediment of the Canadian Beaufort Sea. The THg ranged between 32 and 63 μg/kg and the trace metals such as Fe, Al, Mn, and Zn were significant in distributions. The pH, SO42-, Fe2+, and redox proxy metals were crucial factors in the spatial and vertical heterogeneity of geochemical distributions. CH4 was detected only at the mud volcano site. Microbial analyses identified Clostridium, Desulfosporosinus, Desulfofustis, and Desulftiglans as the predominant Hg methylators and sulfate reducers; Nitrosopumilus and Hyphomicrobium as the major nitrifiers and denitrifiers; Methanosarcina and Methanosaeta as keystone methanogens; and Methyloceanibacter and Methyloprofundus as signature methanotrophs. Altogether, this study expands the current understanding of the microbiological and geochemical features and could be helpful in predicting ecosystem functions in the Canadian Beaufort Sea.

Zoothamnium mariella sp. nov., a marine, colonial ciliate with an atypcial growth pattern, and its ectosymbiont Candidatus Fusimicrobium zoothamnicola gen. nov., sp. nov

Ciliates are unicellular eukaryotes, regularly involved in symbiotic associations. Symbionts may colonize the inside of their cells as well as their surface as ectosymbionts. Here, we report on a new ciliate species, designated as Zoothamnium mariella sp. nov. (Peritrichia, Sessilida), discovered in the northern Adriatic Sea (Mediterranean Sea) in 2021. We found this ciliate species to be monospecifically associated with a new genus of ectosymbiotic bacteria, here proposed as Candidatus Fusimicrobium zoothamnicola gen. nov., sp. nov. To formally describe the new ciliate species, we investigated its morphology and sequenced its 18S rRNA gene. To demonstrate its association with a single species of bacterial ectosymbiont, we performed 16S rRNA gene sequencing, fluorescence in situ hybridization, and scanning electron microscopy. Additionally, we explored the two partners' cultivation requirements and ecology. Z. mariella sp. nov. was characterized by a colony length of up to 1 mm. A consistent number of either seven or eight long branches alternated on the stalk in close distance to each other. The colony developed three different types of zooids: microzooids ("trophic stage"), macrozooids ("telotroch stage"), and terminal zooids ("dividing stage"). Viewed from inside the cell, the microzooids' oral ciliature ran in 1 ¼ turns in a clockwise direction around the peristomial disc before entering the infundibulum, where it performed another ¾ turn. Phylogenetic analyses assigned Z. mariella sp. nov. to clade II of the family Zoothamnidae. The ectosymbiont formed a monophyletic clade within the Gammaproteobacteria along with two other ectosymbionts of peritrichous ciliates and a free-living vent bacterium. It colonized the entire surface of its ciliate host, except for the most basal stalk of large colonies, and exhibited a single, spindle-shaped morphotype. Furthermore, the two partners together appear to be generalists of temperate, oxic, marine shallow-water environments and were collectively cultivable in steady flow-through systems.

Shifts in the coral microbiome in response to in situ experimental deoxygenation

IMPORTANCE

Marine hypoxia is a threat for corals but has remained understudied in tropical regions where coral reefs are abundant. Though microbial symbioses can alleviate the effects of ecological stress, we do not yet understand the taxonomic or functional response of the coral microbiome to hypoxia. In this study, we experimentally lowered oxygen levels around Siderastrea siderea and Agaricia lamarcki colonies in situ to observe changes in the coral microbiome in response to deoxygenation. Our results show that hypoxia triggers a stochastic change of the microbiome overall, with some bacterial families changing deterministically after just 48 hours of exposure. These families represent an increase in anaerobic and opportunistic taxa in the microbiomes of both coral species. Thus, marine deoxygenation destabilizes the coral microbiome and increases bacterial opportunism. This work provides novel and fundamental knowledge of the microbial response in coral during hypoxia and may provide insight into holobiont function during stress.

Depth-dependent microbial communities potentially mediating mercury methylation and various geochemical processes in anthropogenically affected sediments

Metal contamination and other geochemical alterations affect microbial composition and functional activities, disturbing natural biogeochemical cycles. Therefore, it is essential to understand the influences of multi-metal and geochemical interactions on microbial communities. This work investigated the distributions of total mercury (THg), methylmercury (MeHg), and trace metals in the anthropogenically affected sediment. The microbial communities and functional genes profiles were further determined to explore their association with Hg-methylation and geochemical features. The levels of THg and MeHg in sediment cores ranged between 10 and 40 mg/kg and 0.01-0.16 mg/kg, respectively, with an increasing trend toward bottom horizons. The major metals present at all depths were Al, Fe, Mn, and Zn. The enrichment and contamination indices confirmed that the trace metals were highly enriched in the anthropogenically affected sediment. Various functional genes were detected in all strata, indicating the presence of active microbial metabolic processes. The microbial community profiles revealed that the phyla Proteobacteria, Bacteroidetes, Bathyarchaeota, and Euryarchaeota, and the genera Thauera, Woeseia, Methanomethylovorans, and Methanosarcina were the dominant microbes. Correlating major taxa with geochemical variables inferred that sediment geochemistry substantially affects microbial community and biogeochemical cycles. Furthermore, archaeal methanogens and the bacterial phyla Chloroflexi and Firmicutes may play crucial roles in enhancing MeHg levels. Overall, these findings shed new light on the microbial communities potentially involved in Hg-methylation process and other biogeochemical cycles.

Temperature sensitivity of methanogenesis and anaerobic methane oxidation in thermokarst lakes modulated by surrounding vegetation on the Qinghai-Tibet Plateau

Understanding the balance between methane (CH4) production (methanogenesis) and its oxidation is important for predicting carbon emissions from thermokarst lakes under global warming. However, the response of thermokarst lake methanogenesis and the anaerobic oxidation of methane (AOM) to warming, especially from Qinghai-Tibetan Plateau (QTP), is still not quantified. In this study, sediments were collected from 11 thermokarst lakes on the QTP. These lakes are surrounded with different vegetation types, including alpine desert (AD), alpine steppe (AS), alpine meadow (AM) and alpine swamp meadow (ASM). The results showed that methanogenesis and AOM rates exponentially increased with temperature, while the temperature sensitivity (Q10, average Q10 values of methanogenesis and AOM were 0.69-30 and 0.54-16.9 respectively) of methanogenesis were larger than AOM, but not significant, showing a similar temperature dependence of methanogenesis and AOM in thermokarst lake sediments. Thermokarst lake sediments in the ASM had higher methanogenesis and anaerobic oxidation potential, matching its higher NDVI and relative abundances of methanogens and SBM (syntrophic bacteria with methanogens). Although the thermokarst lake sediments AOM depleted 15 %-27.8 % of the total CH4 production, the AOM rate was lower than methanogenesis in thermokarst lake sediments, it did not offset increased CH4 production under anaerobic conditions. The increase in CH4 production in thermokarst lake sediments will likely lead to higher emissions within a warming world. These findings indicate that methanogenesis and AOM in thermokarst lake sediments are sensitive to climate change. Models should consider the Q10 values of methanogenesis and AOM and vegetation types when predicting carbon cycle in thermokarst lakes under global warming.

Potential for the anaerobic oxidation of benzene and naphthalene in thermophilic microorganisms from the Guaymas Basin

Unsubstituted aromatic hydrocarbons (UAHs) are recalcitrant molecules abundant in crude oil, which is accumulated in subsurface reservoirs and occasionally enters the marine environment through natural seepage or human-caused spillage. The challenging anaerobic degradation of UAHs by microorganisms, in particular under thermophilic conditions, is poorly understood. Here, we established benzene- and naphthalene-degrading cultures under sulfate-reducing conditions at 50°C and 70°C from Guaymas Basin sediments. We investigated the microorganisms in the enrichment cultures and their potential for UAH oxidation through short-read metagenome sequencing and analysis. Dependent on the combination of UAH and temperature, different microorganisms became enriched. A Thermoplasmatota archaeon was abundant in the benzene-degrading culture at 50°C, but catabolic pathways remained elusive, because the archaeon lacked most known genes for benzene degradation. Two novel species of Desulfatiglandales bacteria were strongly enriched in the benzene-degrading culture at 70°C and in the naphthalene-degrading culture at 50°C. Both bacteria encode almost complete pathways for UAH degradation and for downstream degradation. They likely activate benzene via methylation, and naphthalene via direct carboxylation, respectively. The two species constitute the first thermophilic UAH degraders of the Desulfatiglandales. In the naphthalene-degrading culture incubated at 70°C, a Dehalococcoidia bacterium became enriched, which encoded a partial pathway for UAH degradation. Comparison of enriched bacteria with related genomes from environmental samples indicated that pathways for benzene degradation are widely distributed, while thermophily and capacity for naphthalene activation are rare. Our study highlights the capacities of uncultured thermophilic microbes for UAH degradation in petroleum reservoirs and in contaminated environments.

Long-term warming modulates diversity, vertical structuring of microbial communities, and sulfate reduction in coastal Baltic Sea sediments

Coastal waters such as those found in the Baltic Sea already suffer from anthropogenic related problems including increased algal blooming and hypoxia while ongoing and future climate change will likely worsen these effects. Microbial communities in sediments play a crucial role in the marine energy- and nutrient cycling, and how they are affected by climate change and shape the environment in the future is of great interest. The aims of this study were to investigate potential effects of prolonged warming on microbial community composition and nutrient cycling including sulfate reduction in surface (∼0.5 cm) to deeper sediments (∼ 24 cm). To investigate this, 16S rRNA gene amplicon sequencing was performed, and sulfate concentrations were measured and compared between sediments in a heated bay (which has been used as a cooling water outlet from a nearby nuclear power plant for approximately 50 years) and a nearby but unaffected control bay. The results showed variation in overall microbial diversity according to sediment depth and higher sulfate flux in the heated bay compared to the control bay. A difference in vertical community structure reflected increased relative abundances of sulfur oxidizing- and sulfate reducing bacteria along with a higher proportion of archaea, such as Bathyarchaeota, in the heated compared to the control bay. This was particularly evident closer to the sediment surface, indicating a compression of geochemical zones in the heated bay. These results corroborate findings in previous studies and additionally point to an amplified effect of prolonged warming deeper in the sediment, which could result in elevated concentrations of toxic compounds and greenhouse gases closer to the sediment surface.

Effect of temperature change on the performance of the hybrid linear flow channel reactor and its implications on sulphate-reducing and sulphide-oxidising microbial community dynamics

Semi-passive bioremediation is a promising strategy to mitigate persistent low volume mine-impacted wastewater containing high sulphate concentrations. Building on the proof of concept demonstration of the hybrid linear flow channel reactor (LFCR), capable of simultaneous biological sulphate reduction and partial sulphide oxidation with elemental sulphur recovery, the impact of key operating parameters, such as temperature, on process performance is critical to real-world application. Temperature fluctuates seasonally and across the diurnal cycle, impacting biological sulphate reduction (BSR) and partial sulphide oxidation. The process is reliant on the metabolic activity and synergistic interactions between sulphate-reducing (SRB) and sulphide-oxidising (SOB) microbial communities that develop within discrete oxic and anoxic microenvironments within the hybrid LFCR. In this study, the impact of operating temperature on process performance was evaluated by decreasing temperature with time from 30 to 10°C in each of three laboratory-scaled hybrid LFCR units operating in pseudo-steady state at 1 g/L sulphate. Using lactate as a carbon source, two reactor sizes (2 and 8 L) were considered, while the impact of lactate vs. acetate as carbon source was evaluated in the 2 L reactors. On incremental decrease in temperature from 30 to 10°C, a decrease in volumetric sulphate reduction rate was observed: from 0.144 to 0.059 mmol/L.h in the 2 L lactate-fed reactor; from 0.128 to 0.042 mmol/L.h in the 8 L lactate-fed reactor; and from 0.127 to 0.010 mmol/L.h in the 2 L acetate-fed reactor. Similarly, sulphate conversion efficiency decreased (2 L lactate-fed: 66% to 27%; 8 L lactate-fed: 61% to 20%; 2 L acetate-fed: 61% to 5%). A decrease in temperature below the critical value (15°C) led to considerable loss in metabolic activity and overall BSR performance. Sessile and planktonic microbial communities were represented by bacterial phyla including Proteobacteria, Synergistetes, Bacteroidetes, and Firmicutes. A diverse group of putative SRB (Deltaproteobacteria) and SOB, including Alpha, Beta, Gamma, and Epsilonproteobacteria phylotypes, were prevalent and shifted in relative abundance and community composition in response to decreasing temperature. Specifically, the decrease in the relative abundance of Deltaproteobacteria with decreasing temperature below 15°C corresponded with a loss of BSR performance across all three reactors. This study demonstrated the impact of low temperature on the physiological selection and ecological differentiation of SRB and SOB communities within the hybrid LFCR and its implications for real-world process performance.

Organic matter biomarker and 13C NMR characteristics of soil and sediment standard reference materials from China

Soil and sediment organic matter (OM) in terrestrial environments represent two critical organic carbon pools on Earth and are likely subject to distinct degrees of oxidation and modification. However, few studies have identified critical molecular-level characteristics that differentiate soil and sediment OM from various climate zones. Using biomarkers and solid-state ¹³C nuclear magnetic resonance (NMR) spectroscopy analyses, we studied the OM characteristics of 11 soil and 7 sediment standard reference materials (SRMs) originating from various geographical locations in China. Results showed significantly higher concentrations of lignin phenols in sediment OM than in soil OM, which may result from protection by higher contents of CaO and less microbial degradation in sediments. Nevertheless, the relative abundances of solvent-extractable lipids (alkanes, alkanols, and alkanoic acids) and ester-bound cutin and suberin biomarkers did not differ significantly between soil and sediment SRMs. The concentrations of lignin biomarkers decreased with increasing weathering degree of the soil, while cutin biomarkers increased with mean annual temperature and precipitation. This phenomenon was not observed in sediment SRMs. This study reveals the distinct OM characteristics between Chinese soil and sediment SRMs and provides fundamental data for future studies to link OM characteristics and functions.

Shifts in benthic bacterial communities associated with farming stages and a microbiological proxy for assessing sulfidic sediment conditions at fish farms

To assess the aquaculture-induced sediment conditions associated with sulfur cycles, shifts in bacterial communities across farming stages were investigated. The sulfate reduction rate (SRR), and concentrations of acid volatile sulfide (AVS) and H₂S were significantly higher at the mid- and post-farming stages than at the early stage, indicating that the aquaculture effects persist even after harvest. Incomplete organic carbon-oxidizing sulfate-reducing bacteria (IO-SRB) affiliated with Desulfobulbaceae, and gammaproteobacterial sulfur oxidizing bacteria (SOB) (Thiohalobacter, Thioprofundum, and Thiohalomonas) were dominant during the early stage, whereas fermenting bacteria (Bacteroidetes and Firmicutes) and complete oxidizing SRB (CO-SRB) belonging to Desulfobacteraceae, and epsilonproteobacterial SOB (Sulfurovum) dominated during the mid- and post-stages. The shift in SRB and SOB communities well reflected the anoxic and sulfidic conditions of farm sediment. Especially, the Sulfurovum-like SOB correlated highly and positively with H₂S, AVS, and SRR, suggesting that they could be relevant microbiological proxies to assess sulfidic conditions in farm sediment.

Microbial Hydrocarbon Degradation in Guaymas Basin-Exploring the Roles and Potential Interactions of Fungi and Sulfate-Reducing Bacteria

Hydrocarbons are degraded by specialized types of bacteria, archaea, and fungi. Their occurrence in marine hydrocarbon seeps and sediments prompted a study of their role and their potential interactions, using the hydrocarbon-rich hydrothermal sediments of Guaymas Basin in the Gulf of California as a model system. This sedimented vent site is characterized by localized hydrothermal circulation that introduces seawater sulfate into methane- and hydrocarbon-rich sediments, and thus selects for diverse hydrocarbon-degrading communities of which methane, alkane- and aromatics-oxidizing sulfate-reducing bacteria and archaea have been especially well-studied. Current molecular and cultivation surveys are detecting diverse fungi in Guaymas Basin hydrothermal sediments, and draw attention to possible fungal-bacterial interactions. In this Hypothesis and Theory article, we report on background, recent results and outcomes, and underlying hypotheses that guide current experiments on this topic in the Edgcomb and Teske labs in 2021, and that we will revisit during our ongoing investigations of bacterial, archaeal, and fungal communities in the deep sedimentary subsurface of Guaymas Basin.

Enrichment of psychrophilic and acidophilic sulfate-reducing bacterial consortia - a solution toward acid mine drainage treatment in cold regions

Failure of sulfate-reducing bacteria (SRB)-mediated treatment of acid mine drainage (AMD) in cold regions due to inhibition of bacteria by acidic pH and low temperature can be overcome by enriching psychrophilic and acidophilic microbial consortia from local metal-rich sediments. In this study, we enriched microbial consortia from Arctic mine sediments at varying pH (3-7) and temperatures (15-37 °C) under anaerobic conditions with repeated sub-culturing in three successive stages, and analyzed the microbial community using 16S rRNA gene sequencing. The enriched SRB genera resulted in high sulfate reduction (85-88%), and significant metal removal (49-99.9%) during the initial stages (stage 1 and 2). Subsequently, sub-culturing the inoculum at pH 3-4.5 resulted in lower sulfate reduction (9-34%) due to the inhibition of SRB by accumulated acetic acid (0.3-9 mM). The microbial metabolic interactions for successful sulfate and metal removal involved initial glycerol co-fermentation to acetic acid at acidic pH (by Desulfosporosinus, Desulfotomaculum, Desulfurospora, and fermentative bacteria including Cellulomonas and Anaerovorax), followed by acetic acid oxidation to CO₂ and H₂ (by Desulfitobacterium) at neutral pH, and subsequent H₂ utilization (by Desulfosporosinus). The results, including the structural and functional properties of enriched microbial consortia, can inform the development of effective biological treatment strategies for AMD in cold regions.

Sulfidic acetate mineralization at 45°C by an aquifer microbial community: key players and effects of heat changes on activity and community structure

High-Temperature Aquifer Thermal Energy Storage (HT-ATES) is a sustainable approach for integrating thermal energy from various sources into complex energy systems. Temperatures ≥45°C, which are relevant in impact zones of HT-ATES systems, may dramatically influence the structure and activities of indigenous aquifer microbial communities. Here, we characterized an acetate-mineralizing, sulfate-reducing microbial community derived from an aquifer and adapted to 45°C. Acetate mineralization was strongly inhibited at temperatures ≤25°C and 60°C. Prolonged incubation at 12°C and 25°C resulted in acetate mineralization recovery after 40-80 days whereas acetate was not mineralized at 60°C within 100 days. Cultures pre-grown at 45°C and inhibited for 28 days by incubation at 12°C, 25°C, or 60°C recovered quickly after changing the temperature back to 45°C. Phylotypes affiliated to the order Spirochaetales and to endospore-forming sulfate reducers of the order Clostridiales were highly abundant in microcosms being active at 45°C highlighting their key role. In summary, prolonged incubation at 45°C resulted in active microbial communities mainly consisting of organisms adapted to temperatures between the typical temperature range of mesophiles and thermophiles and being resilient to temporary heat changes.

Depth profiles of geochemical features, geochemical activities and biodiversity of microbial communities in marine sediments from the Shenhu area, the northern South China Sea

The biogeochemical processes, anaerobic oxidation of methane (AOM) and methanogenesis, control methane emission and create distinct geochemical profiles with depth in marine sediments. Correlating the capacities and biodiversity of the microbial communities in marine sediments remains challenging. We therefore investigated the geochemical constituents and the capabilities and diversity of microbial communities in sediments at different depths in two cores from the Shenhu area in the northern South China Sea, which is characterized by underlying gas hydrates. The geochemical features, sulfate concentration decreased linearly and the acid volatile sulfur accumulated from 4 m below the seafloor (mbsf) to the bottom, indicating significant sulfate reduction. However, the methane concentration was relatively low and showed irregular trends, indicating that our study cores did not reach the sulfate-methane transition zone (SMTZ). Nevertheless, incubation experiments showed that the microbial groups in sediments performed AOM and methanogenesis in the region where sulfate decreased linearly above the SMTZ. We mapped the diversity and abundance of microbial communities in sediments with depth using high-throughput sequencing. A small proportion of known methanogens (<0.3%) may have been responsible for the methanogenesis during incubation. No classical archaeal anaerobic methanotroph (ANME) sequences were detected across all samples; only a small amount of SEEP-SRB1 were detected, and their abundance did not increase with increasing depth. Thus, unknown or unconventional phylotypes may have participated in AOM during the incubation, and the dominant phylum Bathyarchaeota or the small number of detected methanogens are the most likely performers of AOM.

Persistence of atrazine and trifluralin in a clay loam soil undergoing different temperature and moisture conditions

Dissipation kinetics of atrazine and trifluralin in a clay loam soil was investigated in a laboratory incubation experiment under different temperature and moisture conditions. The soil was spiked with diluted atrazine and trifluralin concentrations at 4.50 and 4.25 mg/kg soil, respectively, the moisture content adjusted to 40, 70, and 100% of field capacity (FC) and then incubated in three climatic chambers at 10, 20, and 30 °C. For each of the herbicides, soil samples were collected at 0, 7, 21, 42, 70, and 105 days and analysed by Gas Chromatography-Electron Capture Detector (GC-ECD). A stochastic gamma model was used to model the dissipation of herbicides from the clay loam soil by incorporating environmental factors as covariates to determine half-life and days to complete dissipation. Results showed that temperature played a greater role on atrazine persistence than soil moisture; while the interaction effect of temperature and moisture was significant on the persistence of trifluralin over time. Atrazine dissipated more rapidly at 30 °C compared to 10 and 20 °C, with a half-life of 7.50 days and 326.23 days to reach complete dissipation. Rapid loss of trifluralin was observed at 70% moisture content when incubated at 30 °C, with a half-life of 5.80 days and 182.01 days to complete dissipation. It was observed that the half-life of both herbicides tended to double with every 10 °C decreases of temperature over the range tested. The model indicated that both atrazine and trifluralin have the potential to persist in clay loam soil for several years at temperature ≤20 °C; which could potentially affect following crops in rotation.

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.

The Impact of Methane on Microbial Communities at Marine Arctic Gas Hydrate Bearing Sediment

Cold seeps are characterized by high biomass, which is supported by the microbial oxidation of the available methane by capable microorganisms. The carbon is subsequently transferred to higher trophic levels. South of Svalbard, five geological mounds shaped by the formation of methane gas hydrates, have been recently located. Methane gas seeping activity has been observed on four of them, and flares were primarily concentrated at their summits. At three of these mounds, and along a distance gradient from their summit to their outskirt, we investigated the eukaryotic and prokaryotic biodiversity linked to 16S and 18S rDNA. Here we show that local methane seepage and other environmental conditions did affect the microbial community structure and composition. We could not demonstrate a community gradient from the summit to the edge of the mounds. Instead, a similar community structure in any methane-rich sediments could be retrieved at any location on these mounds. The oxidation of methane was largely driven by anaerobic methanotrophic Archaea-1 (ANME-1) and the communities also hosted high relative abundances of sulfate reducing bacterial groups although none demonstrated a clear co-occurrence with the predominance of ANME-1. Additional common taxa were observed and their abundances were likely benefiting from the end products of methane oxidation. Among these were sulfide-oxidizing Campilobacterota, organic matter degraders, such as Bathyarchaeota, Woesearchaeota, or thermoplasmatales marine benthic group D, and heterotrophic ciliates and Cercozoa.

Impacts of Anthropogenic Pollutants on Benthic Prokaryotic Communities in Mediterranean Touristic Ports

Ports and marinas are central nodes in transport network and play a strategic role in coastal development. They receive pollution from land-based sources, marine traffic and port infrastructures on one side and constitute a potential pollution source for the adjacent coastal areas on the other. The aim of the present study was to evaluate the effects of organic and inorganic co-contamination on the prokaryotic communities in sediments from three Mediterranean ports. The structure and composition of the bacterial and archaeal communities were assessed by targeted metagenomic analysis of the 16S rRNA gene, and the links of prokaryotic communities with environmental and pollution variables were investigated. The harbors presented pronounced site-specificity in the environmental properties and pollution status. Consistently, the structure of archaeal and bacterial communities in surface sediments exhibited a strong spatial variation among the three investigated ports. On the contrary, a wide overlap in composition of prokaryotic assemblages among sites was found, but local variation in the community composition and loss of prokaryotic diversity was highlighted in a heavily impacted port sector near a shipyard. We provided evidences that organic matter, metals and PAHs as well as temperature and salinity play a strong role in structuring benthic bacterial communities significantly contributing to the understanding of their responses to anthropogenic perturbations in marine coastal areas. Among metals, copper was recognized as strongly associated with the observed changes in bacterial assemblages. Overall, this study provides the first assessment of the effects exerted by multiple organic and inorganic contaminations on benthic prokaryotes in ports over a large spatial scale and designates bacterial community as a candidate tool for the monitoring of the sediment quality status in harbors.

Influence of Human Activities on Broad-Scale Estuarine-Marine Habitats Using Omics-Based Approaches Applied to Marine Sediments

Rapid urban expansion and increased human activities have led to the progressive deterioration of many marine ecosystems. The diverse microbial communities that inhabit these ecosystems are believed to influence large-scale geochemical processes and, as such, analyzing their composition and functional metabolism can be a means to assessing an ecosystem’s resilience to physical and chemical perturbations, or at the very least provide baseline information and insight into future research needs. Here we show the utilization of organic and inorganic contaminant screening coupled with metabolomics and bacterial 16S rRNA gene sequencing to assess the microbial community structure of marine sediments and their functional metabolic output. The sediments collected from Moreton Bay (Queensland, Australia) contained low levels of organic and inorganic contaminants, typically below guideline levels. The sequencing dataset suggest that sulfur and nitrite reduction, dehalogenation, ammonia oxidation, and xylan degradation were the major metabolic functions. The community metabolites suggest a level of functional homogeneity down the 40-cm core depth sampled, with sediment habitat identified as a significant driver for metabolic differences. The communities present in river and sandy channel samples were found to be the most active, with the river habitats likely to be dominated by photoheterotrophs that utilized carbohydrates, fatty acids and alcohols as well as reduce nitrates to release atmospheric nitrogen and oxidize sulfur. Bioturbated mud habitats showed overlapping faunal activity between riverine and sandy ecosystems. Nitrogen-fixing bacteria and lignin-degrading bacteria were most abundant in the sandy channel and bioturbated mud, respectively. The use of omics-based approaches provide greater insight into the functional metabolism of these impacted habitats, extending beyond discrete monitoring to encompassing whole community profiling that represents true phenotypical outputs. Ongoing omics-based monitoring that focuses on more targeted pathway analyses is recommended in order to quantify the flux changes within these systems and establish variations from these baseline measurements.

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.

Dynamics of Sulfate-Reducing Bacteria Community Structure in Surface Sediment of a Seasonally Hypoxic Enclosed Bay

We herein report on the dynamics of a sulfate-reducing bacteria (SRB) community structure in the surface sediment of a seasonally hypoxic enclosed bay for two consecutive years (2012 and 2013). The uppermost (0–5 mm) and subsurface (5–10 mm) layers of sediment were examined with a terminal-restriction fragment length polymorphism (T-RFLP) analysis based on the dissimilatory sulfite reductase (dsrA) gene. The SRB community significantly differed between the two sediment layers over the sampling period. This difference was mainly attributed to operational taxonomic units (OTUs) that were unique to either of the sediment layers. However, nearly 70% of total OTUs were shared between the two layers, with a few predominating. Therefore, no significant shift was observed in the SRB community structure under varying dissolved oxygen (DO) conditions in bottom water overlying the sediment surface. An additional analysis of 16S rRNA gene amplicon sequences, conducted for three uppermost sediment samples (July, August, and September in 2012), revealed that Desulfococcus, a member of SRB with high tolerance to oxygen, was the predominant Deltaproteobacteria across the uppermost sediment samples. Based on the predominance of shared OTUs across the SRB community in the sediment (0–10 mm) regardless of bottom-water DO, some SRB that are physiologically tolerant of a wide range of DO conditions may have dominated and masked changes in responsive SRB to DO concentrations. These results suggest that the SRB community structure in the enclosed bay became stable under repeated cycles of seasonal hypoxia, but may be compromised if the severity of hypoxia increases in the future.

Single-Cell Genomics Reveals a Diverse Metabolic Potential of Uncultivated Desulfatiglans-Related Deltaproteobacteria Widely Distributed in Marine Sediment

Desulfatiglans-related organisms comprise one of the most abundant deltaproteobacterial lineages in marine sediments where they occur throughout the sediment column in a gradient of increasing sulfate and organic carbon limitation with depth. Characterized Desulfatiglans isolates are dissimilatory sulfate reducers able to grow by degrading aromatic hydrocarbons. The ecophysiology of environmental Desulfatiglans-populations is poorly understood, however, possibly utilization of aromatic compounds may explain their predominance in marine subsurface sediments. We sequenced and analyzed seven Desulfatiglans-related single-cell genomes (SAGs) from Aarhus Bay sediments to characterize their metabolic potential with regard to aromatic compound degradation and energy metabolism. The average genome assembly size was 1.3 Mbp and completeness estimates ranged between 20 and 50%. Five of the SAGs (group 1) originated from the sulfate-rich surface part of the sediment while two (group 2) originated from sulfate-depleted subsurface sediment. Based on 16S rRNA gene amplicon sequencing group 2 SAGs represent the more frequent types of Desulfatiglans-populations in Aarhus Bay sediments. Genes indicative of aromatic compound degradation could be identified in both groups, but the two groups were metabolically distinct with regard to energy conservation. Group 1 SAGs carry a full set of genes for dissimilatory sulfate reduction, whereas the group 2 SAGs lacked any genetic evidence for sulfate reduction. The latter may be due to incompleteness of the SAGs, but as alternative energy metabolisms group 2 SAGs carry the genetic potential for growth by acetogenesis and fermentation. Group 1 SAGs encoded reductive dehalogenase genes, allowing them to access organohalides and possibly conserve energy by their reduction. Both groups possess sulfatases unlike their cultured relatives allowing them to utilize sulfate esters as source of organic carbon and sulfate. In conclusion, the uncultivated marine Desulfatiglans populations are metabolically diverse, likely reflecting different strategies for coping with energy and sulfate limitation in the subsurface seabed.

Bacterial interactions during sequential degradation of cyanobacterial necromass in a sulfidic arctic marine sediment

Seafloor microorganisms impact global carbon cycling by mineralizing vast quantities of organic matter (OM) from pelagic primary production, which is predicted to increase in the Arctic because of diminishing sea ice cover. We studied microbial interspecies-carbon-flow during anaerobic OM degradation in arctic marine sediment using stable isotope probing. We supplemented sediment incubations with 13 C-labeled cyanobacterial necromass (spirulina), mimicking fresh OM input, or acetate, an important OM degradation intermediate and monitored sulfate reduction rates and concentrations of volatile fatty acids (VFAs) during substrate degradation. Sequential 16S rRNA gene and transcript amplicon sequencing and fluorescence in situ hybridization combined with Raman microspectroscopy revealed that only few bacterial species were the main degraders of 13 C-spirulina necromass. Psychrilyobacter, Psychromonas, Marinifilum, Colwellia, Marinilabiaceae and Clostridiales species were likely involved in the primary hydrolysis and fermentation of spirulina. VFAs, mainly acetate, produced from spirulina degradation were mineralized by sulfate-reducing bacteria and an Arcobacter species. Cellular activity of Desulfobacteraceae and Desulfobulbaceae species during acetoclastic sulfate reduction was largely decoupled from relative 16S rRNA gene abundance shifts. Our findings provide new insights into the identities and physiological constraints that determine the population dynamics of key microorganisms during complex OM degradation in arctic marine sediments.© 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Low Energy Subsurface Environments as Extraterrestrial Analogs

Earth's subsurface is often isolated from phototrophic energy sources and characterized by chemotrophic modes of life. These environments are often oligotrophic and limited in electron donors or electron acceptors, and include continental crust, subseafloor oceanic crust, and marine sediment as well as subglacial lakes and the subsurface of polar desert soils. These low energy subsurface environments are therefore uniquely positioned for examining minimum energetic requirements and adaptations for chemotrophic life. Current targets for astrobiology investigations of extant life are planetary bodies with largely inhospitable surfaces, such as Mars, Europa, and Enceladus. Subsurface environments on Earth thus serve as analogs to explore possibilities of subsurface life on extraterrestrial bodies. The purpose of this review is to provide an overview of subsurface environments as potential analogs, and the features of microbial communities existing in these low energy environments, with particular emphasis on how they inform the study of energetic limits required for life. The thermodynamic energetic calculations presented here suggest that free energy yields of reactions and energy density of some metabolic redox reactions on Mars, Europa, Enceladus, and Titan could be comparable to analog environments in Earth's low energy subsurface habitats.

Application of Proton-Transfer-Reaction Mass Spectrometry (PTR-MS) and 33S Isotope Labeling for Monitoring Sulfur Processes in Livestock Waste

Reduced sulfur compounds emitted from livestock production cause odor nuisance for local residents. The microbial processes responsible for this are not well described in swine manure and a method for monitoring the biological processes is necessary to develop strategic abatement technologies. In this study, Proton-Transfer-Reaction Mass Spectrometry and isotope-labeled sulfate were combined and applied to elucidate the sulfur processes in swine manure with high time resolution. We successfully monitored reduction of isotope ³³S labeled sulfate into corresponding ³³S hydrogen sulfide and found that some of the ³³S hydrogen sulfide was further methylated into ³³S methanethiol. The isotope patterns in reduced sulfur compounds together with usage of inhibitors enabled us to calculate a sulfate reduction rate of 1.03 ± 0.18 mM/day equivalent to 76.9 ± 3.0% of total hydrogen sulfide emissions. Cysteine degradation constituted 20.2 ± 2.7% of the total hydrogen sulfide produced and the remaining hydrogen sulfide came from demethylation of methanethiol and dimethyl sulfide. Another source to methanethiol, besides hydrogen sulfide methylation, was methionine degradation, which contributed with 78.3 ± 2.5% of the methanethiol production, whereas the remaining 21.7 ± 2.5% came from hydrogen sulfide methylation. This study suggests, therefore, that emissions of odorous sulfur compounds from swine manure can be reduced by inhibiting methionine degradation and sulfate reduction.

The life sulfuric: microbial ecology of sulfur cycling in marine sediments

Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular- and ecosystem-level processes. Sulfur-transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate-rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep-subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle.