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

Organic matter degradation in the deep, sulfidic waters of the Black Sea: insights into the ecophysiology of novel anaerobic bacteria

BACKGROUND

Recent studies have reported the identity and functions of key anaerobes involved in the degradation of organic matter (OM) in deep (> 1000 m) sulfidic marine habitats. However, due to the lack of available isolates, detailed investigation of their physiology has been precluded. In this study, we cultivated and characterized the ecophysiology of a wide range of novel anaerobes potentially involved in OM degradation in deep (2000 m depth) sulfidic waters of the Black Sea.

RESULTS

We have successfully cultivated a diverse group of novel anaerobes belonging to various phyla, including Fusobacteriota (strain S5), Bacillota (strains A1T and A2), Spirochaetota (strains M1T, M2, and S2), Bacteroidota (strains B1T, B2, S6, L6, SYP, and M2P), Cloacimonadota (Cloa-SY6), Planctomycetota (Plnct-SY6), Mycoplasmatota (Izemo-BS), Chloroflexota (Chflx-SY6), and Desulfobacterota (strains S3T and S3-i). These microorganisms were able to grow at an elevated hydrostatic pressure of up to 50 MPa. Moreover, this study revealed that different anaerobes were specialized in degrading specific types of OM. Strains affiliated with the phyla Fusobacteriota, Bacillota, Planctomycetota, and Mycoplasmatota were found to be specialized in the degradation of cellulose, cellobiose, chitin, and DNA, respectively, while strains affiliated with Spirochaetota, Bacteroidota, Cloacimonadota, and Chloroflexota preferred to ferment less complex forms of OM. We also identified members of the phylum Desulfobacterota as terminal oxidizers, potentially involved in the consumption of hydrogen produced during fermentation. These results were supported by the identification of genes in the (meta)genomes of the cultivated microbial taxa which encode proteins of specific metabolic pathways. Additionally, we analyzed the composition of membrane lipids of selected taxa, which could be critical for their survival in the harsh environment of the deep sulfidic waters and could potentially be used as biosignatures for these strains in the sulfidic waters of the Black Sea.

CONCLUSIONS

This is the first report that demonstrates the cultivation and ecophysiology of such a diverse group of microorganisms from any sulfidic marine habitat. Collectively, this study provides a step forward in our understanding of the microbes thriving in the extreme conditions of the deep sulfidic waters of the Black Sea. Video Abstract.

Secondary production and priming reshape the organic matter composition in marine sediments

Organic matter (OM) transformations in marine sediments play a crucial role in the global carbon cycle. However, secondary production and priming have been ignored in marine biogeochemistry. By incubating shelf sediments with various 13C-labeled algal substrates for 400 days, we show that ~65% of the lipids and ~20% of the proteins were mineralized by numerically minor heterotrophic bacteria as revealed by RNA stable isotope probing. Up to 11% of carbon from the algal lipids was transformed into the biomass of secondary producers as indicated by 13C incorporation in amino acids. This biomass turned over throughout the experiment, corresponding to dynamic microbial shifts. Algal lipid addition accelerated indigenous OM degradation by 2.5 to 6 times. This priming was driven by diverse heterotrophic bacteria and sulfur- and iron-cycling bacteria and, in turn, resulted in extra secondary production, which exceeded that stimulated by added substrates. These interactions between degradation, secondary production, and priming govern the eventual fate of OM in marine sediments.

Seasonality in land-ocean connectivity and local processes control sediment bacterial community structure and function in a High Arctic tidal flat

Climate change is altering patterns of precipitation, cryosphere thaw, and land-ocean influxes, affecting understudied Arctic estuarine tidal flats. These transitional zones between terrestrial and marine systems are hotspots for biogeochemical cycling, often driven by microbial processes. We investigated surface sediment bacterial community composition and function from May to September along a river-intertidal-subtidal-fjord gradient. We paired metabarcoding of in situ communities with in vitro carbon-source utilization assays. Bacterial communities differed in space and time, alongside varying environmental conditions driven by local seasonal processes and riverine inputs, with salinity emerging as the dominant structuring factor. Terrestrial and riverine taxa were found throughout the system, likely transported with runoff. In vitro assays revealed sediment bacteria utilized a broader range of organic matter substrates when incubated in fresh and brackish water compared to marine water. These results highlight the importance of salinity for ecosystem processes in these dynamic tidal flats, with the highest potential for utilization of terrestrially derived organic matter likely limited to tidal flat areas (and times) where sediments are permeated by freshwater. Our results demonstrate that intertidal flats must be included in future studies on impacts of increased riverine discharge and transport of terrestrial organic matter on coastal carbon cycling in a warming Arctic.

Distinct gut microbial communities and functional predictions in divergent ophiuroid species: host differentiation, ecological niches, and adaptation to cold-water habitats

IMPORTANCE

Gastrointestinal microorganisms are critical to the survival and adaptation of hosts, and there are few studies on the differences and functions of gastrointestinal microbes in widely distributed species. This study investigated the gut microbes of two ophiuroid species (Ophiura sarsii and its subspecies O. sarsii vadicola) in cold-water habitats of the Northern Pacific Ocean. The results showed that a combination of host and environmental factors shapes the intestinal microbiota of ophiuroids. There was a high similarity in microbial communities between the two groups living in different regions, which may be related to their similar ecological niches. These microorganisms played a vital role in the ecological success of ophiuroids as the foundation for their adaptation to cold-water environments. This study revealed the complex relationship between hosts and their gut microbes, providing insights into the role they play in the adaptation and survival of marine species.

Identification and cultivation of anaerobic bacterial scavengers of dead cells

The cycle of life and death and Earth's carbon cycle(s) are intimately linked, yet how bacterial cells, one of the largest pools of biomass on Earth, are recycled back into the carbon cycle remains enigmatic. In particular, no bacteria capable of scavenging dead cells in oxygen-depleted environments have been reported thus far. In this study, we discover the first anaerobes that scavenge dead cells and the two isolated strains use distinct strategies. Based on live-cell imaging, transmission electron microscopy, and hydrolytic enzyme assays, one strain (designated CYCD) relied on cell-to-cell contact and cell invagination for degrading dead food bacteria where as the other strain (MGCD) degraded dead food bacteria via excretion of lytic extracellular enzymes. Both strains could degrade dead cells of differing taxonomy (bacteria and archaea) and differing extents of cell damage, including those without artificially inflicted physical damage. In addition, both depended on symbiotic metabolic interactions for maximizing cell degradation, representing the first cultured syntrophic Bacteroidota. We collectively revealed multiple symbiotic bacterial decomposition routes of dead prokaryotic cells, providing novel insight into the last step of the carbon cycle.

Genomic and metabolic insights into the first host-associated isolate of Psychrilyobacter

Although gut bacteria are vital to their hosts, few studies have focused on marine animals. Psychrilyobacter is frequently related to various marine animals, but its interaction with host remains unknown due to the lack of host-associated isolate or genomic information. Here, we combined cultivation-independent and cultivation-dependent methods to uncover the potential roles of Psychrilyobacter in the host abalone. The high-throughput sequencing and literature compiling results indicated that Psychrilyobacter is widely distributed in marine and terrestrial ecosystems with both host-associated and free-living lifestyles, but with a strong niche preference in the guts of marine invertebrates, especially abalone. By in vitro enrichment that mimicked the gut inner environment, the first host-related pure culture of Psychrilyobacter was isolated from the abalone intestine. Phylogenetic, physiological, and biochemical characterizations suggested that it represents a novel species named Psychrilyobacter haliotis B1. Carbohydrate utilization experiments and genomic evidence indicated that B1 can utilize diverse host-food-related monosaccharides and disaccharides but not polysaccharides, implying its potential role in the downstream fermentation instead of the upstream food degradation in the gut. Particularly, this strain showed potential to colonize the gut and benefit the host via different strategies, such as the short-chain fatty acids generation by fermenting peptides and/or amino acids, and the putative production of diverse vitamins and antibiotics to support the host growth and antipathogenicity. To our knowledge, strain B1 represents the first host-related pure culture of Psychrilyobacter; genomic and metabolic evidence showed some beneficial characteristics of the dominant gut anaerobe to the host. IMPORTANCE Psychrilyobacter is a globally distributed bacterial genus and with an inhabiting preference for guts of marine invertebrates. Due to the difficulty of cultivation and the limited genomic information, its role in host remains largely unknown. We isolated the first host-associated Psychrilyobacter species from abalone gut and uncovered its functional potential to the host through different mechanisms. Our findings provide some insights into the understanding of host-microbe interactions on a core taxon with the marine invertebrates, and the isolate may have an application potential in the protection of marine animals.

Deciphering community interactions of sulfate-reducing microorganisms in complex microbial communities of marine sediments

Sulfate-reducing microorganisms (SRM) are key players in global sulfur and carbon cycles, especially in anoxic marine sediments. They are critical in anaerobic food webs because they consume fermentation products like volatile fatty acids (VFAs) and/or hydrogen produced from other microbes that degrade organic matter. Apart from this, the interplay between SRM and other coexisting microorganisms is poorly understood. A recent study by Liang et al. provides intriguing new insights about how the activity of SRM influence microbial communities. Using an elegant combination of microcosm experiments, community ecology, genomics, and in vitro studies, they provide evidence that SRM are central in ecological networks and community assembly, and interestingly, that the control of pH by SRM activity has a substantial impact on other key bacteria, like members of the Marinilabiliales (Bacteroidota). This work has important implications for understanding how marine sediment microbes function together to provide important ecosystem services like recycling organic matter.

Influence of sedimentary deposition on the microbial assembly process in Arctic Holocene marine sediments

The sea-level rise during the Holocene (11-0 ky BP) and its resulting sedimentation and biogeochemical processes may control microbial life in Arctic sediments. To gain further insight into this interaction, we investigated a sediment core (up to 10.7 m below the seafloor) from the Chuckchi Shelf of the western Arctic Ocean using metabarcoding-based sequencing and qPCR to characterize archaeal and bacterial 16S rRNA gene composition and abundance, respectively. We found that Arctic Holocene sediments harbor local microbial communities, reflecting geochemical and paleoclimate separations. The composition of bacterial communities was more diverse than that of archaeal communities, and specifically distinct at the boundary layer of the sulfate-methane transition zone. Enriched cyanobacterial sequences in the Arctic middle Holocene (8-7 ky BP) methanogenic sediments remarkably suggest past cyanobacterial blooms. Bacterial communities were phylogenetically influenced by interactions between dispersal limitation and environmental selection governing community assembly under past oceanographic changes. The relative influence of stochastic and deterministic processes on the bacterial assemblage was primarily determined by dispersal limitation. We have summarized our findings in a conceptual model that revealed how changes in paleoclimate phases cause shifts in ecological succession and the assembly process. In this ecological model, dispersal limitation is an important driving force for progressive succession for bacterial community assembly processes on a geological timescale in the western Arctic Ocean. This enabled a better understanding of the ecological processes that drive the assembly of communities in Holocene sedimentary habitats affected by sea-level rise, such as in the shallow western Arctic shelves.

Aerotolerant Thiosulfate-Reducing Bacterium Fusibacter sp. Strain WBS Isolated from Littoral Bottom Sediments of the White Sea-Biochemical and Genome Analysis

The strain WBS, an anaerobic, psychro- and halotolerant bacterium belonging to the genus Fusibacter, was isolated from the littoral bottom sediments of the White Sea, Arctic, Russia. Fusibacter bizertensis WBS grew at temperatures between 8 and 32 °C (optimum growth at 18-20 °C), pH between 5.2 and 8.3 (optimum growth at pH 7.2), and at NaCl concentrations between 0 and 70 g L^-1 (optimum growth at 32 g L^-1). It reduced sulfate, thiosulfate, and elemental sulfur into sulfide, and, probably, the strain is able to disproportionate thiosulfate. The strain also utilized a wide range of substrates as it is a chemoorganotrophic bacterium. Analysis of the sequenced genome revealed genes for all enzymes involved in the Embden-Meyerhof glycolytic pathway as well as genes for the non-oxidative stage of the pentose phosphate pathway. The presence of genes encoding aldehyde dehydrogenases and alcohol dehydrogenases also suggests that, in addition to acetate, alcohols can also be the fermentation products. The strain possessed superoxide dismutase and peroxidase activities and the ability to consume O₂, which is in full accordance with the presence of corresponding genes of antioxidant defense in the genome. The phylogenetic analysis suggested that the strain WBS is the closest relative of Fusibacter bizertensis LTF Kr01^T (16S rRNA gene sequence similarity 98.78%). Based on biochemical and genomic characteristics, the strain WBS is proposed to represent a novel aero-, halo- and psychrotolerant strain from the genus Fusibacter, isolated for the first time among its members from cold oxygenated marine bottom sediments.

Microbial communities associated with kelp detritus in temperate and subantarctic intertidal sediments

Kelp forests, among the most productive ecosystems on Earth, cover large areas of the South Atlantic coast. Sediment heterotrophic bacteria have a pivotal role in the degradation of kelp biomass, however, the response of sediment microbial communities to periodic kelp biomass inputs is mostly unknown. Here, we show that kelp biomass induced rapid changes in overlying water chemistry and shifts in sediment microbial communities, which differed in the experimental systems containing Macrocystis pyrifera (M) and Undaria pinnatifida (U) with sediments of the respective regions. We observed results compatible with the degradation of labile, high molecular weight compounds into smaller and more refractory compounds towards the end of the incubations. The capability of microbial communities to degrade alginate, the major component of kelp cell walls, significantly increased with respect to controls after kelp biomass addition (Absorbance at 235 nm 1.2 ± 0.3 and 1.0 ± 0.2 for M and U, respectively, controls <0.2, t = 4 days). Shifts in microbial community structure (based on 16S rRNA gene amplicon sequencing) were tightly related to the kelp treatment and, to a lesser extent, to the sediment provenance (Principal Coordinates Analysis, 80 % of variation explained in the first two axes). Dissolved oxygen, pH, salinity, alginolytic potential, Absorbance at 235 and 600 nm, total N, total C, and SUVA index correlated significantly with community structure. Differentially abundant populations between kelp-amended treatments and controls included members of the Flavobacteriia class (Algibacter and Polaribacter), and Gammaproteobacteria (Psychromonas and Marinomonas), among others. Metagenomes of M and U-amended sediments contained sequences from 18 of the 19 enzyme families related to alginate or fucoidan degradation. Specific taxonomic groups were associated with enzyme classes targeting different substrates, suggesting niche differentiation. This work expands our knowledge on the patterns of microbial assemblages from intertidal sediments in response to kelp biomass inputs.

Bacterial Necromass Is Rapidly Metabolized by Heterotrophic Bacteria and Supports Multiple Trophic Levels of the Groundwater Microbiome

Pristine groundwater is a highly stable environment with microbes adapted to dark, oligotrophic conditions. Input events like heavy rainfalls can introduce the excess particulate organic matter, including surface-derived microorganisms, thereby disturbing the groundwater microbiome. Some surface-derived bacteria will not survive this translocation, leading to an input of necromass to the groundwater. Here, we investigated the effects of necromass addition to the microbial community in fractured bedrock groundwater, using groundwater mesocosms as model systems. We followed the uptake of ¹³C-labeled necromass by the bacterial and eukaryotic groundwater community quantitatively and over time using a complementary protein-stable and DNA-stable isotope probing approach. Necromass was rapidly depleted in the mesocosms within 4 days, accompanied by a strong decrease in Shannon diversity and a 10-fold increase in bacterial 16S rRNA gene copy numbers. Species of Flavobacterium, Massilia, Rheinheimera, Rhodoferax, and Undibacterium dominated the microbial community within 2 days and were identified as key players in necromass degradation, based on a ¹³C incorporation of >90% in their peptides. Their proteomes comprised various proteins for uptake and transport functions and amino acid metabolization. After 4 and 8 days, the autotrophic and mixotrophic taxa Nitrosomonas, Limnohabitans, Paucibacter, and Acidovorax increased in abundance with a ¹³C incorporation between 0.5% and 23%. Likewise, eukaryotes assimilated necromass-derived carbon either directly or indirectly. Our data point toward a fast and exclusive uptake of labeled necromass by a few specialists followed by a concerted action of groundwater microorganisms, including autotrophs presumably fueled by released, reduced nitrogen and sulfur compounds generated during necromass degradation.

IMPORTANCE Subsurface microbiomes provide essential ecosystem services, like the generation of drinking water. These ecosystems are devoid of light-driven primary production, and microbial life is adapted to the resulting oligotrophic conditions. Modern groundwater is most vulnerable to anthropogenic and climatic impacts. Heavy rainfalls, which will increase with climate change, can result in high surface inputs into shallow aquifers by percolation or lateral flow. These inputs include terrestrial organic matter and surface-derived microbes that are not all capable to flourish in aquatic subsurface habitats. Here, we investigated the response of groundwater mesocosms to the addition of bacterial necromass, simulating event-driven surface input. We found that the groundwater microbiome responds with a rapid bloom of only a few primary degraders, followed by the activation of typical groundwater autotrophs and mixotrophs, as well as eukaryotes. Our results suggest that this multiphase strategy is essential to maintain the balance of the groundwater microbiome to provide ecosystem services.

Microbial Activities and Selection from Surface Ocean to Subseafloor on the Namibian Continental Shelf

Oxygen minimum zones (OMZs) are hot spots for redox-sensitive nitrogen transformations fueled by sinking organic matter. In comparison, the regulating role of sulfur-cycling microbes in marine OMZs, their impact on carbon cycling in pelagic and benthic habitats, and activities below the seafloor remain poorly understood. Using ¹³C DNA stable isotope probing (SIP) and metatranscriptomics, we explored microbial guilds involved in sulfur and carbon cycling from the ocean surface to the subseafloor on the Namibian shelf. There was a clear separation in microbial community structure across the seawater-seafloor boundary, which coincided with a 100-fold-increased concentration of microbial biomass and unique gene expression profiles of the benthic communities. ¹³C-labeled 16S rRNA genes in SIP experiments revealed carbon-assimilating taxa and their distribution across the sediment-water interface. Most of the transcriptionally active taxa among water column communities that assimilated ¹³C from diatom exopolysaccharides (mostly Bacteroidetes, Actinobacteria, Alphaproteobacteria, and Planctomycetes) also assimilated ¹³C-bicarbonate under anoxic conditions in sediment incubations. Moreover, many transcriptionally active taxa from the seafloor community (mostly sulfate-reducing Deltaproteobacteria and sulfide-oxidizing Gammaproteobacteria) that assimilated ¹³C-bicarbonate under sediment anoxic conditions also assimilated ¹³C from diatom exopolysaccharides in the surface ocean and OMZ waters. Despite strong selection at the sediment-water interface, many taxa related to either planktonic or benthic communities were found to be present at low abundance and actively assimilating carbon under both sediment and water column conditions. In austral winter, mixing of shelf waters reduces stratification and suspends sediments from the seafloor into the water column, potentially spreading metabolically versatile microbes across niches.

IMPORTANCE Microbial activities in oxygen minimum zones (OMZs) transform inorganic fixed nitrogen into greenhouse gases, impacting the Earth’s climate and nutrient equilibrium. Coastal OMZs are predicted to expand with global change and increase carbon sedimentation to the seafloor. However, the role of sulfur-cycling microbes in assimilating carbon in marine OMZs and related seabed habitats remain poorly understood. Using ¹³C DNA stable isotope probing and metatranscriptomics, we explore microbial guilds involved in sulfur and carbon cycling from ocean surface to subseafloor on the Namibian shelf. Despite strong selection and differential activities across the sediment-water interface, many active taxa were identified in both planktonic and benthic communities, either fixing inorganic carbon or assimilating organic carbon from algal biomass. Our data show that many planktonic and benthic microbes linked to the sulfur cycle can cross redox boundaries when mixing of the shelf waters reduces stratification and suspends seafloor sediment particles into the water column.

Phylogenetic diversity and spatiotemporal dynamics of bacterial and microeukaryotic plankton communities in Gwangyang Bay of the Korean Peninsula

Nutrient dynamics function globally, flowing from rivers to the ocean (estuarine–coastal zone), and are vulnerable to climate change. Microbial habitats can be affected by marine nutrient dynamics and may provide a clue to predict microbial responses to environmental heterogeneity in estuarine–coastal zones. We surveyed surface seawater in Gwangyang Bay, a semi-enclosed estuary in Korea, from 2016 to 2018 using a metabarcoding approach with prokaryotic 16S and eukaryotic 18S rRNA genes. Bacterial and microeukaryotic communities in these waters showed distinct local communities in response to environmental heterogeneity and community transition at spatiotemporal scales in the estuarine–coastal zone. The relative abundance of prokaryotic and eukaryotic operational taxonomic units suggested a microbial trophic interaction in the Gwangyang Bay waters. We found that the community assembly process in prokaryotic communities was primarily influenced by biological interaction (immigration–emigration), whereas that in eukaryotic communities was more affected by environmental stress (habitat specificity) rather than by biotic factors. Our findings in the Gwangyang Bay waters may provide information on underlying (biotic or abiotic) factors of the assembly process in microbial communities in the estuarine–coastal zone.

The physiology and metabolic properties of a novel, low-abundance Psychrilyobacter species isolated from the anoxic Black Sea shed light on its ecological role

Members of the Psychrilyobacter spp. of the phylum Fusobacteria have been recently suggested to be amongst the most significant primary degraders of the detrital organic matter in sulfidic marine habitats, despite representing only a small proportion (<0.1%) of the microbial community. In this study, we have isolated a previously uncultured Psychrilyobacter species (strains SD5^T and BL5; Psychrilyobacter piezotolerans sp. nov.) from the sulfidic waters (i.e., 2000 m depth) of the Black Sea and investigated its physiology and genomic capability in order to better understand potential ecological adaptation strategies. P. piezotolerans utilized a broad range of organic substituents (carbohydrates and proteins) and, remarkably, grew at sulfide concentrations up to 32 mM. These flexible physiological properties were supported by the presence of the respective metabolic pathways in the genomes of both strains. Growth at varying hydrostatic pressure (0.1-50 MPa) was sustained by modifying its membrane lipid composition. Thus, we have isolated a novel member of the 'rare biosphere', which endures the extreme conditions and may play a significant role in the degradation of detrital organic matter sinking into the sulfidic waters of the Black Sea.

Comparative Study of the Gut Microbiota Among Four Different Marine Mammals in an Aquarium

Despite an increasing appreciation in the importance of host–microbe interactions in ecological and evolutionary processes, information on the gut microbial communities of some marine mammals is still lacking. Moreover, whether diet, environment, or host phylogeny has the greatest impact on microbial community structure is still unknown. To fill part of this knowledge gap, we exploited a natural experiment provided by an aquarium with belugas (Delphinapterus leucas) affiliated with family Monodontidae, Pacific white-sided dolphins (Lagenorhynchus obliquidens) and common bottlenose dolphin (Tursiops truncatus) affiliated with family Delphinidae, and Cape fur seals (Arctocephalus pusillus pusillus) affiliated with family Otariidae. Results show significant differences in microbial community composition of whales, dolphins, and fur seals and indicate that host phylogeny (family level) plays the most important role in shaping the microbial communities, rather than food and environment. In general, the gut microbial communities of dolphins had significantly lower diversity compared to that of whales and fur seals. Overall, the gut microbial communities were mainly composed of Firmicutes and Gammaproteobacteria, together with some from Bacteroidetes, Fusobacteria, and Epsilonbacteraeota. However, specific bacterial lineages were differentially distributed among the marine mammal groups. For instance, Lachnospiraceae, Ruminococcaceae, and Peptostreptococcaceae were the dominant bacterial lineages in the gut of belugas, while for Cape fur seals, Moraxellaceae and Bacteroidaceae were the main bacterial lineages. Moreover, gut microbial communities in both Pacific white-sided dolphins and common bottlenose dolphins were dominated by a number of pathogenic bacteria, including Clostridium perfringens, Vibrio fluvialis, and Morganella morganii, reflecting the poor health condition of these animals. Although there is a growing recognition of the role microorganisms play in the gut of marine mammals, current knowledge about these microbial communities is still severely lacking. Large-scale research studies should be undertaken to reveal the roles played by the gut microbiota of different marine mammal species.

Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling

Acidobacteriota are widespread and often abundant in marine sediments, yet their metabolic and ecological properties are poorly understood. Here, we examined metabolisms and distributions of Acidobacteriota in marine sediments of Svalbard by functional predictions from metagenome-assembled genomes (MAGs), amplicon sequencing of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes and transcripts, and gene expression analyses of tetrathionate-amended microcosms. Acidobacteriota were the second most abundant dsrB-harboring (averaging 13%) phylum after Desulfobacterota in Svalbard sediments, and represented 4% of dsrB transcripts on average. Meta-analysis of dsrAB datasets also showed Acidobacteriota dsrAB sequences are prominent in marine sediments worldwide, averaging 15% of all sequences analysed, and represent most of the previously unclassified dsrAB in marine sediments. We propose two new Acidobacteriota genera, Candidatus Sulfomarinibacter (class Thermoanaerobaculia, "subdivision 23") and Ca. Polarisedimenticola ("subdivision 22"), with distinct genetic properties that may explain their distributions in biogeochemically distinct sediments. Ca. Sulfomarinibacter encode flexible respiratory routes, with potential for oxygen, nitrous oxide, metal-oxide, tetrathionate, sulfur and sulfite/sulfate respiration, and possibly sulfur disproportionation. Potential nutrients and energy include cellulose, proteins, cyanophycin, hydrogen, and acetate. A Ca. Polarisedimenticola MAG encodes various enzymes to degrade proteins, and to reduce oxygen, nitrate, sulfur/polysulfide and metal-oxides. 16S rRNA gene and transcript profiling of Svalbard sediments showed Ca. Sulfomarinibacter members were relatively abundant and transcriptionally active in sulfidic fjord sediments, while Ca. Polarisedimenticola members were more relatively abundant in metal-rich fjord sediments. Overall, we reveal various physiological features of uncultured marine Acidobacteriota that indicate fundamental roles in seafloor biogeochemical cycling.

Macroalgae degradation promotes microbial iron reduction via electron shuttling in coastal Antarctic sediments

Colonization of newly ice-free areas by marine benthic organisms intensifies burial of macroalgae detritus in Potter Cove coastal surface sediments (Western Antarctic Peninsula). Thus, fresh and labile macroalgal detritus serves as primary organic matter (OM) source for microbial degradation. Here, we investigated the effects on post-depositional microbial iron reduction in Potter Cove using sediment incubations amended with pulverized macroalgal detritus as OM source, acetate as primary product of OM degradation and lepidocrocite as reactive iron oxide to mimic in situ conditions. Humic substances analogue anthraquinone-2,6-disulfonic acid (AQDS) was also added to some treatments to simulate potential for electron shuttling. Microbial iron reduction was promoted by macroalgae and further enhanced by up to 30-folds with AQDS. Notably, while acetate amendment alone did not stimulate iron reduction, adding macroalgae alone did. Acetate, formate, lactate, butyrate and propionate were detected as fermentation products from macroalgae degradation. By combining 16S rRNA gene sequencing and RNA stable isotope probing, we reconstructed the potential microbial food chain from macroalgae degraders to iron reducers. Psychromonas, Marinifilum, Moritella, and Colwellia were detected as potential fermenters of macroalgae and fermentation products such as lactate. Members of class deltaproteobacteria including Sva1033, Desulfuromonas, and Desulfuromusa together with Arcobacter (former phylum Epsilonbacteraeota, now Campylobacterota) acted as dissimilatory iron reducers. Our findings demonstrate that increasing burial of macroalgal detritus in an Antarctic fjord affected by glacier retreat intensifies early diagenetic processes such as iron reduction. Under scenarios of global warming, the active microbial populations identified above will expand their environmental function, facilitate OM remineralisation, and contribute to an increased release of iron and CO₂ from sediments. Such indirect consequences of glacial retreat are often overlooked but might, on a regional scale, be relevant for the assessment of future nutrient and carbon fluxes.

Cross-Shore and Depth Zonations in Bacterial Diversity Are Linked to Age and Source of Dissolved Organic Matter across the Intertidal Area of a Sandy Beach

Microbial communities and dissolved organic matter (DOM) are intrinsically linked within the global carbon cycle. Demonstrating this link on a molecular level is hampered by the complexity of both counterparts. We have now investigated this connection within intertidal beach sediments, characterized by a runnel-ridge system and subterranean groundwater discharge. Using datasets generated by Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and Ilumina-sequencing of 16S rRNA genes, we predicted metabolic functions and determined links between bacterial communities and DOM composition. Four bacterial clusters were defined, reflecting differences within the community compositions. Those were attributed to distinct areas, depths, or metabolic niches. Cluster I was found throughout all surface sediments, probably involved in algal-polymer degradation. In ridge and low water line samples, cluster III became prominent. Associated porewaters indicated an influence of terrestrial DOM and the release of aromatic compounds from reactive iron oxides. Cluster IV showed the highest seasonality and was associated with species previously reported from a subsurface bloom. Interestingly, Cluster II harbored several members of the candidate phyla radiation (CPR) and was related to highly degraded DOM. This may be one of the first geochemical proofs for the role of candidate phyla in the degradation of highly refractory DOM.

Organic Matter Type Defines the Composition of Active Microbial Communities Originating From Anoxic Baltic Sea Sediments

Carbon cycling in anoxic marine sediments is dependent on uncultured microbial communities. Niches of heterotrophic microorganisms are defined by organic matter (OM) type and the different phases in OM degradation. We investigated how OM type defines microbial communities originating from organic-rich, anoxic sediments from the Baltic Sea. We compared changes in the sediment microbial community, after incubation with different stable isotope labeled OM types [i.e., particulate algal organic matter (PAOM), protein, and acetate], by using DNA stable isotope probing (DNA-SIP). Incorporation of 13C and/or 15N label was predominantly detected in members of the phyla Planctomycetes and Chloroflexi, which also formed the majority (>50%) of the original sediment community. While these phylum-level lineages incorporated label from all OM types, phylogenetic analyses revealed a niche separation at the order level. Members of the MSBL9 (Planctomycetes), the Anaerolineales (Chloroflexi), and the class Bathyarchaeota, were identified as initial degraders of carbohydrate-rich OM, while other uncultured orders, like the CCM11a and Phycisphaerales (Planctomycetes), Dehalococcoidia, and JG30-KF-CM66 (Chloroflexi), incorporated label also from protein and acetate. Our study highlights the importance of initial fermentation of complex carbon pools in shaping anoxic sediment microbial communities and reveals niche specialization at the order level for the most important initial degraders in anoxic sediments.

Shifting the microbiome of a coral holobiont and improving host physiology by inoculation with a potentially beneficial bacterial consortium

Background

The coral microbiome plays a key role in host health by being involved in energy metabolism, nutrient cycling, and immune system formation. Inoculating coral with beneficial bacterial consortia may enhance the ability of this host to cope with complex and changing marine environments. In this study, the coral Pocillopora damicornis was inoculated with a beneficial microorganisms for corals (BMC) consortium to investigate how the coral host and its associated microbial community would respond.

Results

High-throughput 16S rRNA gene sequencing revealed no significant differences in bacterial community α-diversity. However, the bacterial community structure differed significantly between the BMC and placebo groups at the end of the experiment. Addition of the BMC consortium significantly increased the relative abundance of potentially beneficial bacteria, including the genera Mameliella and Endozoicomonas. Energy reserves and calcification rates of the coral host were also improved by the addition of the BMC consortium. Co-occurrence network analysis indicated that inoculation of coral with the exogenous BMC consortium improved the physiological status of the host by shifting the coral-associated microbial community structure.

Conclusions

Manipulating the coral-associated microbial community may enhance the physiology of coral in normal aquarium conditions (no stress applied), which may hypothetically contribute to resilience and resistance in this host.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02167-5.

Microbial responses to herbivory-induced vegetation changes in a high-Arctic peatland

Herbivory by barnacle geese (Branta leucopsis) alters the vegetation cover and reduces ecosystem productivity in high-Arctic peatlands, limiting the carbon sink strength of these ecosystems. Here we investigate how herbivory-induced vegetation changes affect the activities of peat soil microbiota using metagenomics, metatranscriptomics and targeted metabolomics in a comparison of fenced exclosures and nearby grazed sites. Our results show that a different vegetation with a high proportion of vascular plants developed due to reduced herbivory, resulting in a larger and more diverse input of polysaccharides to the soil at exclosed study sites. This coincided with higher sugar and amino acid concentrations in the soil at this site as well as the establishment of a more abundant and active microbiota, including saprotrophic fungi with broad substrate ranges, like Helotiales (Ascomycota) and Agaricales (Basidiomycota). A detailed description of fungal transcriptional profiles revealed higher gene expression for cellulose, hemicellulose, pectin, lignin and chitin degradation at herbivory-exclosed sites. Furthermore, we observed an increase in the number of genes and transcripts for predatory eukaryotes such as Entomobryomorpha (Arthropoda). We conclude that in the absence of herbivory, the development of a vascular vegetation alters the soil polysaccharide composition and supports larger and more active populations of fungi and predatory eukaryotes.

Anaerobic bacterial degradation of protein and lipid macromolecules in subarctic marine sediment

Microorganisms in marine sediments play major roles in marine biogeochemical cycles by mineralizing substantial quantities of organic matter from decaying cells. Proteins and lipids are abundant components of necromass, yet the taxonomic identities of microorganisms that actively degrade them remain poorly resolved. Here, we revealed identities, trophic interactions, and genomic features of bacteria that degraded 13C-labeled proteins and lipids in cold anoxic microcosms containing sulfidic subarctic marine sediment. Supplemented proteins and lipids were rapidly fermented to various volatile fatty acids within 5 days. DNA-stable isotope probing (SIP) suggested Psychrilyobacter atlanticus was an important primary degrader of proteins, and Psychromonas members were important primary degraders of both proteins and lipids. Closely related Psychromonas populations, as represented by distinct 16S rRNA gene variants, differentially utilized either proteins or lipids. DNA-SIP also showed 13C-labeling of various Deltaproteobacteria within 10 days, indicating trophic transfer of carbon to putative sulfate-reducers. Metagenome-assembled genomes revealed the primary hydrolyzers encoded secreted peptidases or lipases, and enzymes for catabolism of protein or lipid degradation products. Psychromonas species are prevalent in diverse marine sediments, suggesting they are important players in organic carbon processing in situ. Together, this study provides new insights into the identities, functions, and genomes of bacteria that actively degrade abundant necromass macromolecules in the seafloor.

Anoxic chlorophyll maximum enhances local organic matter remineralization and nitrogen loss in Lake Tanganyika

In marine and freshwater oxygen-deficient zones, the remineralization of sinking organic matter from the photic zone is central to driving nitrogen loss. Deep blooms of photosynthetic bacteria, which form the suboxic/anoxic chlorophyll maximum (ACM), widespread in aquatic ecosystems, may also contribute to the local input of organic matter. Yet, the influence of the ACM on nitrogen and carbon cycling remains poorly understood. Using a suite of stable isotope tracer experiments, we examined the transformation of nitrogen and carbon under an ACM (comprising of Chlorobiaceae and Synechococcales) and a non-ACM scenario in the anoxic zone of Lake Tanganyika. We find that the ACM hosts a tight coupling of photo/litho-autotrophic and heterotrophic processes. In particular, the ACM was a hotspot of organic matter remineralization that controlled an important supply of ammonium driving a nitrification-anammox coupling, and thereby played a key role in regulating nitrogen loss in the oxygen-deficient zone.

Enigmatic blooms of phytoplankton in aquatic oxygen-deficient zones could exacerbate depletion of nitrogen. Here the authors perform stable isotope experiments on the oxygen-deficient waters of Lake Tanganyika in Africa, finding that blooms drive down fixed nitrogen and could expand as a result of climate change.

Patterns in Benthic Microbial Community Structure Across Environmental Gradients in the Beaufort Sea Shelf and Slope

The paradigm of tight pelagic-benthic coupling in the Arctic suggests that current and future fluctuations in sea ice, primary production, and riverine input resulting from global climate change will have major impacts on benthic ecosystems. To understand how these changes will affect benthic ecosystem function, we must characterize diversity, spatial distribution, and community composition for all faunal components. Bacteria and archaea link the biotic and abiotic realms, playing important roles in organic matter (OM) decomposition, biogeochemical cycling, and contaminant degradation, yet sediment microbial communities have rarely been examined in the North American Arctic. Shifts in microbial community structure and composition occur with shifts in OM inputs and contaminant exposure, with implications for shifts in ecological function. Furthermore, the characterization of benthic microbial communities provides a foundation from which to build focused experimental research. We assessed diversity and community structure of benthic prokaryotes in the upper 1 cm of sediments in the southern Beaufort Sea (United States and Canada), and investigated environmental correlates of prokaryotic community structure over a broad spatial scale (spanning 1,229 km) at depths ranging from 17 to 1,200 m. Based on hierarchical clustering, we identified four prokaryotic assemblages from the 85 samples analyzed. Two were largely delineated by the markedly different environmental conditions in shallow shelf vs. upper continental slope sediments. A third assemblage was mainly comprised of operational taxonomic units (OTUs) shared between the shallow shelf and upper slope assemblages. The fourth assemblage corresponded to sediments receiving heavier OM loading, likely resulting in a shallower anoxic layer. These sites may also harbor microbial mats and/or methane seeps. Substructure within these assemblages generally reflected turnover along a longitudinal gradient, which may be related to the quantity and composition of OM deposited to the seafloor; bathymetry and the Mackenzie River were the two major factors influencing prokaryote distribution on this scale. In a broader geographical context, differences in prokaryotic community structure between the Beaufort Sea and Norwegian Arctic suggest that benthic microbes may reflect regional differences in the hydrography, biogeochemistry, and bathymetry of Arctic shelf systems.

Artificial consortium demonstrates emergent properties of enhanced cellulosic-sugar degradation and biofuel synthesis

Planktonic cultures, of a rationally designed consortium, demonstrated emergent properties that exceeded the sums of monoculture properties, including a >200% increase in cellobiose catabolism, a >100% increase in glycerol catabolism, a >800% increase in ethanol production, and a >120% increase in biomass productivity. The consortium was designed to have a primary and secondary-resource specialist that used crossfeeding with a positive feedback mechanism, division of labor, and nutrient and energy transfer via necromass catabolism. The primary resource specialist was Clostridium phytofermentans (a.k.a. Lachnoclostridium phytofermentans), a cellulolytic, obligate anaerobe. The secondary-resource specialist was Escherichia coli, a versatile, facultative anaerobe, which can ferment glycerol and byproducts of cellobiose catabolism. The consortium also demonstrated emergent properties of enhanced biomass accumulation when grown as biofilms, which created high cell density communities with gradients of species along the vertical axis. Consortium biofilms were robust to oxic perturbations with E. coli consuming O₂, creating an anoxic environment for C. phytofermentans. Anoxic/oxic cycling further enhanced biomass productivity of the biofilm consortium, increasing biomass accumulation ~250% over the sum of the monoculture biofilms. Consortium emergent properties were credited to several synergistic mechanisms. E. coli consumed inhibitory byproducts from cellobiose catabolism, driving higher C. phytofermentans growth and higher cellulolytic enzyme production, which in turn provided more substrate for E. coli. E. coli necromass enhanced C. phytofermentans growth while C. phytofermentans necromass aided E. coli growth via the release of peptides and amino acids, respectively. In aggregate, temporal cycling of necromass constituents increased flux of cellulose-derived resources through the consortium. The study establishes a consortia-based, bioprocessing strategy built on naturally occurring interactions for improved conversion of cellulose-derived sugars into bioproducts.

Contribution of archaea and bacteria in sustaining climate change by oxidizing ammonia and sulfur in an Arctic Fjord

The present study attempts to investigate the microbial communities and their potential to oxidize ammonia and sulfur at different sites of Arctic Fjord by targeted metagenomics. The high throughput sequencing revealed archaeal Thaumarchaeota (79.3%), Crenarchaeota (10.9%), Euryarchaeota (5.4%), and Woesearchaeota (2.9%) across different depths. In contrast, the bacterial communities depict predominance of Proteobacteria (52.6%), which comprises of dominant genera viz. Sulfurovum (11.2%) and Sulfurimonas (6.3%). Characterizing the metabolic potential of microbial communities with prime focus on the ammonia and sulfur cycling revealed the presence of amoABC and narGHYZ/ nxrAB genes encoding key enzymes. The ammonia cycling coupled with an augmentation of members of Nitrosopumilus belonging to the phylum Thaumarcheaota suggests the vital role of archaeal communities. Similarly, the persistence of chemolithoautotrophic members of Sulfurovum and Sulfurimonas along with the anaerobic genera Desulfocapsa and Desulfobulbus harboring SOX (sulfur-oxidation) system indicates the modulatory role of bacterial communities in sulfur cycling.

Microbial community shift under exposure of dredged sediments from a eutrophic bay

Microbial communities occur in almost every habitat. To evaluate the homeostasis disruption of in situ microbiomes, dredged sediments from Guanabara Bay-Brazil (GB) were mixed with sediments from outside of the bay (D) in three different proportions (25%, 50%, and 75%) which we called GBD25, GBD50, and GBD75. Grain size, TOC, and metals-as indicators of complex contamination-dehydrogenase (DHA) and esterase enzymes (EST)-as indicators of microbial community availability-were determined. Microbial community composition was addressed by amplifying the 16S rRNA gene for DGGE analysis and sequencing using MiSeq platform (Illumina).We applied the quality ratio index (QR) to the GB, D, and every GBD mixture to integrate geochemical parameters with our microbiome data. QR indicated high environmental risk for GB and every GBD mixture, and low risk for D. The community shifted from aerobic to anaerobic profile, consistent with the characteristics of GB. Sample D was dominated by JTB255 marine benthic group, related to low impacted areas. Milano-WF1B-44 was the most representative of GB, often found in anaerobic and sulfur enriched environments. In GBD, the denitrifying sulfur-oxidizing bacteria, Sulfurovum, was the most representative, typically found in suboxic or anoxic niches. The canonical correspondence analysis was able to explain 60% of the community composition variation and exhibit the decrease of environmental quality as the contamination increases. Physiological and taxonomic shifts of the microbial assemblage in sediments were inferred by QR, which was suitable to determine sediment risk. The study produced sufficient information to improve the dredging plan and management.

Marine mercury-methylating microbial communities from coastal to Capbreton Canyon sediments (North Atlantic Ocean)

Microbial mercury (Hg) methylation transforms inorganic mercury to neurotoxic methylmercury (MeHg) mainly in aquatic anoxic environments. Sampling challenges in marine ecosystems, particularly in submarine canyons, leads to a lack of knowledge about the Hg methylating microbia in marine sediments. A previous study showed an enrichment of mercury species in sediments from the Capbreton Canyon where both geochemical parameters and microbial activities constrained the net MeHg production. In order to characterize Hg-methylating microbial communities from coastal to deeper sediments, we analysed the diversity of microorganisms' (16S rDNA-based sequencing) and Hg methylators (hgcA based cloning and sequencing). Both, 16S rDNA and hgcA gene analysis demonstrated that the putative Hg-methylating prokaryotes were likely within the Deltaproteobacteria, dominated by sulfur-compounds based reducing bacteria (mainly sulfate reducers). Additionally, others clades were also identified as carrying HgcA gene, such as, Chloroflexi, Spirochaetes, Elusimicrobia, PVC superphylum (Plantomycetes, Verrucomicrobia and Chlamydiae) and Euryarchaea. Nevertheless, 61% of the hgcA sequences were not assigned to specific clade, indicating that further studies are needed to understand the implication of new microorganisms carrying hgcA in the Hg methylation in marine environments. These first results suggest that sulfur cycle drives the Hg-methylation in marine ecosystem.

Next-generation physiology approaches to study microbiome function at single cell level

The function of cells in their native habitat often cannot be reliably predicted from genomic data or from physiology studies of isolates. Traditional experimental approaches to study the function of taxonomically and metabolically diverse microbiomes are limited by their destructive nature, low spatial resolution or low throughput. Recently developed technologies can offer new insights into cellular function in natural and human-made systems and how microorganisms interact with and shape the environments that they inhabit. In this Review, we provide an overview of these next-generation physiology approaches and discuss how the non-destructive analysis of cellular phenotypes, in combination with the separation of the target cells for downstream analyses, provide powerful new, complementary ways to study microbiome function. We anticipate that the widespread application of next-generation physiology approaches will transform the field of microbial ecology and dramatically improve our understanding of how microorganisms function in their native environment.

Simulating metagenomic stable isotope probing datasets with MetaSIPSim

Background

DNA-stable isotope probing (DNA-SIP) links microorganisms to their in-situ function in diverse environmental samples. Combining DNA-SIP and metagenomics (metagenomic-SIP) allows us to link genomes from complex communities to their specific functions and improves the assembly and binning of these targeted genomes. However, empirical development of metagenomic-SIP methods is hindered by the complexity and cost of these studies. We developed a toolkit, ‘MetaSIPSim,’ to simulate sequencing read libraries for metagenomic-SIP experiments. MetaSIPSim is intended to generate datasets for method development and testing. To this end, we used MetaSIPSim generated data to demonstrate the advantages of metagenomic-SIP over a conventional shotgun metagenomic sequencing experiment.

Results

Through simulation we show that metagenomic-SIP improves the assembly and binning of isotopically labeled genomes relative to a conventional metagenomic approach. Improvements were dependent on experimental parameters and on sequencing depth. Community level G + C content impacted the assembly of labeled genomes and subsequent binning, where high community G + C generally reduced the benefits of metagenomic-SIP. Furthermore, when a high proportion of the community is isotopically labeled, the benefits of metagenomic-SIP decline. Finally, the choice of gradient fractions to sequence greatly influences method performance.

Conclusions

Metagenomic-SIP is a valuable method for recovering isotopically labeled genomes from complex communities. We show that metagenomic-SIP performance depends on optimization of experimental parameters. MetaSIPSim allows for simulation of metagenomic-SIP datasets which facilitates the optimization and development of metagenomic-SIP experiments and analytical approaches for dealing with these data.

Glacial Runoff Promotes Deep Burial of Sulfur Cycling-Associated Microorganisms in Marine Sediments

Marine fjords with active glacier outlets are hot spots for organic matter burial in the sediments and subsequent microbial mineralization. Here, we investigated controls on microbial community assembly in sub-arctic glacier-influenced (GI) and non-glacier-influenced (NGI) marine sediments in the Godthåbsfjord region, south-western Greenland. We used a correlative approach integrating 16S rRNA gene and dissimilatory sulfite reductase (dsrB) amplicon sequence data over six meters of depth with biogeochemistry, sulfur-cycling activities, and sediment ages. GI sediments were characterized by comparably high sedimentation rates and had "young" sediment ages of <500 years even at 6 m sediment depth. In contrast, NGI stations reached ages of approximately 10,000 years at these depths. Sediment age-depth relationships, sulfate reduction rates (SRR), and C/N ratios were strongly correlated with differences in microbial community composition between GI and NGI sediments, indicating that age and diagenetic state were key drivers of microbial community assembly in subsurface sediments. Similar bacterial and archaeal communities were present in the surface sediments of all stations, whereas only in GI sediments were many surface taxa also abundant through the whole sediment core. The relative abundance of these taxa, including diverse Desulfobacteraceae members, correlated positively with SRRs, indicating their active contributions to sulfur-cycling processes. In contrast, other surface community members, such as Desulfatiglans, Atribacteria, and Chloroflexi, survived the slow sediment burial at NGI stations and dominated in the deepest sediment layers. These taxa are typical for the energy-limited marine deep biosphere and their relative abundances correlated positively with sediment age. In conclusion, our data suggests that high rates of sediment accumulation caused by glacier runoff and associated changes in biogeochemistry, promote persistence of sulfur-cycling activity and burial of a larger fraction of the surface microbial community into the deep subsurface.

Uncultured Gammaproteobacteria and Desulfobacteraceae Account for Major Acetate Assimilation in a Coastal Marine Sediment

Acetate is a key intermediate in anaerobic mineralization of organic matter in marine sediments. Its turnover is central to carbon cycling, however, the relative contribution of different microbial populations to acetate assimilation in marine sediments is unknown. To quantify acetate assimilation by in situ abundant bacterial populations, we incubated coastal marine sediments with ¹⁴C-labeled acetate and flow-sorted cells that had been labeled and identified by fluorescence in situ hybridization. Subsequently, scintillography determined the amount of ¹⁴C-acetate assimilated by distinct populations. This approach fostered a high-throughput quantification of acetate assimilation by phylogenetically identified populations. Acetate uptake was highest in the oxic-suboxic surface layer for all sorted bacterial populations, including deltaproteobacterial sulfate-reducing bacteria (SRB), which accounted for up to 32% of total bacterial acetate assimilation. We show that the family Desulfobulbaceae also assimilates acetate in marine sediments, while the more abundant Desulfobacteraceae dominated acetate assimilation despite lower uptake rates. Unexpectedly, members of Gammaproteobacteria accounted for the highest relative acetate assimilation in all sediment layers with up to 31–62% of total bacterial acetate uptake. We also show that acetate is used to build up storage compounds such as polyalkanoates. Together, our findings demonstrate that not only the usual suspects SRB but a diverse bacterial community may substantially contribute to acetate assimilation in marine sediments. This study highlights the importance of quantitative approaches to reveal the roles of distinct microbial populations in acetate turnover.

Effects of organic matter and low oxygen on the mycobenthos in a coastal lagoon

Fungi living in sediments (‘mycobenthos’) are hypothesized to play a role in the degradation of organic matter deposited at the land‐sea interface, but the environmental factors influencing the mycobenthos are poorly understood. We used mock community calibrated Illumina sequencing to show that the mycobenthos community structure in a coastal lagoon was significantly changed after exposure to a lignocellulose extract and subsequent development of benthic anoxia over a relatively short (10 h) incubation. Saprotrophic taxa dominated and were selected for under benthic anoxia, specifically Aquamyces (Chytridiomycota) and Orbilia (Ascomycota), implicating these genera as important benthic saprotrophs. Protein encoding genes involved in energy and biomass production from Fungi and the fungal‐analogue group Labyrinthulomycetes had the highest increase in expression with the added organic matter compared with all other groups, indicating that lignocellulose stimulates metabolic activity in the mycobenthos. Flavobacteria dominated the active bacterial community that grew rapidly with the lignocellulose extract and crashed sharply upon O₂ depletion. Our findings indicate that the diversity, activity and trophic potential of the mycobenthos changes rapidly in response to organic matter and decreasing O₂ concentrations, which together with heterotrophic Flavobacteria, undergo ‘boom and bust’ dynamics during lignocellulose degradation in estuarine ecosystems.