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We report the draft genomes of two morphologically distinct variants of Bacillus subtilis ATCC 6051 [NCBI3610]. The two isolates exhibit differences in not only morphology but also their genetics, despite identical 16S rRNA sequences. Investigating the genetic differences of colony morphology variation in this model organism can provide valuable insights.
Tolumonas sp. WCU1 was cultured from Dicks Creek on the campus of Western Carolina University. Colonies were obtained from water plated on R2A medium. A subculture was isolated and BLAST analysis of the 16S rRNA placed it into the genus Tolumonas, with the highest match at 95.7% percent identity to T. osonensis. Whole genome phylogenetic analysis identified the three species in the genus of Tolumonas to be only 78.1 to 78.5% in average nucleotide identity (ANI). These species include T. auensis , T. osonensis, and T. lignilytica.
We retained 18 MAGs with ≥50% completion and <10% contamination (i.e., at least medium quality). Of these, 10 had >90% completion and <5% contamination; however, only one (Paceibacteria Bin.003_MG) can be described as high-quality, as the others lacked a full suite of 5S, 16S, and 23S rRNA genes. To maximize the diversity of our recovered MAGs, we also retained one MAG (Chromatiaceae Bin.008_AM) with >40% (but less than 50%) completion and <5% contamination, as well as one (Rhodopseudomonas Bin.015_MK) with >90% completion and <20% (but>10%) contamination. Interestingly, significant chimerism was not detected in this MAG (40) , suggesting that the elevated contamination (20%) may instead reflect two closely related strains collapsing into a single bin. Consistent with this, contig coverage was bimodal, with roughly 17% of the assembly at ~115x and the remaining 83% at ~282x, while GC content remained uniform across both groups (~64%), arguing against contamination from a taxonomically distinct source.
This Narrative is part of a collection used in publications focused on the microbial ecology of fjord sediment in the high Arctic, Svalbard. This paper took a genome-centric approach to uncover novel metabolic capabilities of the Acidobacteriota clade. Metagenomic data was coupled with amplicon sequencing of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes, and transcripts (available under NCBI-Genbank Bioproject PRJNA623111), and gene expression analyses of tetrathionate-amended microcosms. This Narrative contains the metagenomic assemblies that were constructed within KBase for reproducibility. These include: stnF metagenome assembly stnAB metagenome assembly stnAC metagenome assembly These metagenome assemblies served as the launching point for an additional publication focused on a different clade of bacteria (Buongiorno et al., 2020). Link to that Narrative landing page here. Please cite: Flieder, Mathias, Joy Buongiorno, Craig W. Herbold, Bela Hausmann, Thomas Rattei, Karen G. Lloyd, Alexander Loy, and Kenneth Wasmund. "Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling." The ISME Journal (2021): 1-22.
The economy of biorefineries is influenced not only by biofuel production from carbohydrates but also by the production of valuable compounds from largely underutilized industrial residues. Currently, the demand for many chemicals that could be made in a biorefinery, such as succinic acid (SA), medium-chain fatty acids (MCFAs), and lactic acid (LA), is fulfilled using petroleum, palm oil, or pure carbohydrates as raw materials, respectively. Thin stillage (TS), the residual liquid material following distillation of ethanol, is an underutilized coproduct from the starch biofuel industry. This carbon-rich material has the potential for chemical upgrading by microorganisms. Here, we explored the formation of different fermentation products by microbial communities grown on TS using different bioreactor conditions. At the baseline operational condition (6-day retention time, pH 5.5, 35°C), we observed a mixture of MCFAs as the principal fermentation products. Operation of a bioreactor with a 1-day retention time induced an increase in SA production, and a temperature increase to 55°C resulted in the accumulation of lactic and propionic acids. In addition, a reactor operated with a 1-day retention time at 55°C conditions resulted in LA accumulation as the main fermentation product. The prominent members of the microbial community in each reactor were assessed by 16S rRNA gene amplicon sequencing and phylogenetic analysis. Under all operating conditions, members of the Lactobacillaceae family within Firmicutes and the Acetobacteraceae family within Proteobacteria were ubiquitous. Members of the Prevotellaceae family within Bacteroidetes and Lachnospiraceae family within the Clostridiales order of Firmicutes were mostly abundant at 35°C and not abundant in the microbial communities of the TS reactors incubated at 55°C. The ability to adjust bioreactor operating conditions to select for microbial communities with different fermentation product profiles offers new strategies to explore and compare potentially valuable fermentation products from TS and allows industries the flexibility to adapt and switch chemical production based on market prices and demands.
Increasing evidence shows that alterations in gut microbiome (GM) contribute to the development of type 2 diabetes mellitus (T2DM), and fecal microbiota transplantation (FMT) successfully treats various human diseases. However, the benefits of FMT therapy to T2DM patients remain unknown. We enrolled 17 patients with T2DM for nonblinded, one-armed intervention trial of FMT. A total of 20 healthy individuals were recruited as the baseline control. HbA1c% and metabolic parameter change were evaluated in 17 T2DM patients 12 weeks after they received FMT from healthy donors. The GM composition was characterized by 16S rRNA gene amplicon sequencing from fecal samples prior to and 12 weeks after FMT treatment. We found that the GM of T2DM patients was reconstituted by FMT. We observed a statistically significant decrease in HbA1c% (from 7.565 ± 0.148 to 7.190 ± 0.210, p<0.01), blood glucose (from 8.483 ± 0.497 to 7.286 ± 0.454 mmol/L, p<0.01), and uric acid (from 309.4 ± 21.5 to 259.1 ± 15.8 µmol/L, p<0.01) while a significant increase in postprandial C-peptide (from 4.503 ± 0.600 to 5.471 ± 0.728 ng/ml, p<0.01) at 12 weeks after FMT. Closely evaluating the changes in these assays, we found individual variability in response to FMT treatment. Out of 17 T2DM patients, 11 were found to significantly improve T2DM symptoms. The FMT responders have significantly higher levels of the family Rikenellaceae and the genus Anaerotruncus (family Ruminococcaceae) in their pretreated fecal in comparison to nonresponders, which could predict the clinical response with an area under the curve of 0.83. Our findings suggest that certain T2DM patients can potentially benefit from FMT, and the pretreated abundance of Rikenellaceae and Anaerotruncus in the fecal of patients may serve as potential biomarkers for selecting T2DM patients to receive FMT.
Soil microbial communities affect the formation of micro-scale mineral-associated organic matter (MAOM) where complex processes, including adhesion, aggregate formation, microbial mineral weathering and soil organic matter stabilization occur in a narrow zone of large biogeochemical gradients. Here we designed a field study to examine carbon stabilization mechanisms by using in-growth mesh bags containing biotite that were placed in a ponderosa pine root zone for 6 months and compared to the surrounding bulk soil. We sought to determine the composition of the microbial community in the mesh bags compared to the surrounding soils, analyze the direct interactions between microbes and biotite, and finally identify the nature of the newly formed MAOM within the mesh-bags. Our results revealed that minerals in the mesh bags were colonized by a microbial community that produced organic matter in situ. The 16S rRNA gene sequencing and ITS2 region characterization showed phylogenetic similarity between the mesh bag and bulk soil archaea/bacteria and fungi microbiomes, with significant differences in alpha- and beta-diversity and species abundances. Organic matter pools in the mesh bags, analyzed by Fourier transform ion cyclotron resonance mass spectrometry, contained protein- (peptides) and lipid-like compounds while the bulk soil OM was comprised of lignin-like and carboxyl-rich alicyclic molecules. These results support that the newly formed biotite associated organic compounds have a microbial signature in the mesh bags. High-resolution electron microscopy documented strongly adhered organic compounds to biotite surfaces, formation of microaggregates, elemental uptake at the microbe (organic matter)-mineral interface, and distortion of biotite layers. Overall, this study shows the direct and indirect involvement of soil microbial communities from the root zone of ponderosa pine in the formation of MAOM, soil organic carbon stabilization, microaggregation, and mineral weathering at micro- and nano-scales.
Dumpsites are reservoirs of persistent organic pollutants (POPs) and heavy metals (HMs), constituting environmental hazards to humanity. Autochthonous microorganisms in dumpsites exhibit various degrees of responses to contaminants. Unfortunately, there is a dearth of information on the types and concentration of pollutants and the array of microorganisms in these dumpsites which may play important roles in the metabolism of such pollutants or other community processes. Therefore, determining the microbial community structure in such contaminated sites across a municipality is essential for profiling the taxa that would serve as consensus degraders of the pollutants. In this study, soil samples from three dumpsites (Cele, CS; Solous, SS; and Computer Village, CVS) were characterized for geochemical properties using GC-MS, MP-AES, and other analytical protocols, while the dynamics of bacterial communities were evaluated based on their 16S rRNA gene barcodes. A significant difference in the bacterial communities was observed among the dumpsites in relation to the extent of pollution caused by POPs and HMs. CVS, with the highest HM contamination, was rich in Actinobacteria (41.7%) and Acidobacteria (10.2%), in contrast to CS and SS. Proteobacteria (34.1%) and Firmicutes (20%) were the dominant phyla in CS (highest POP contamination), while Bacteroidetes (45.5%) and Proteobacteria (39.9%) were dominant in SS soil.Bacilluswas the dominant genus in the most polluted dumpsite. Canonical correspondence analysis revealed that polycyclic aromatic hydrocarbons (PAHs) and HMs shaped the structure of the bacterial operational taxonomic units (OTUs) in the most polluted dumpsite. Out of a total of 706 OTUs, 628 OTUs exhibited a significant correlation (>50%) with benzo(b)fluoranthene, azobenzene, dibenzofurans, pyrene, dibenzo(a,l)pyrene, Cu, and Zn. In particular, Proteobacteria (Achromobactersp. andSerratiasp.), Bacteroidetes (Zhouiasp.), and Firmicutes (Bacillussp.) were suggested to be pivotal to the ecophysiology of dumpsite soils contaminated with POPs and HMs. The results generally underscored the importance of metagenomic and physicochemical analyses of polluted systems in enabling correlations for useful prediction of drivers of such ecosystems. This will further improve our understanding of the metabolic potential and adaptation of organisms in such systems.
Serpentinite-hosted systems represent modern-day analogs of early Earth environments. In these systems, water-rock interactions generate highly alkaline and reducing fluids that can contain hydrogen, methane, and low-molecular-weight hydrocarbons-potent reductants capable of fueling microbial metabolism. In this study, we investigated the microbiota of Hakuba Happo hot springs (~50°C; pH~10.5–11), located in Nagano (Japan), which are impacted by the serpentinization process. Analysis of the 16S rRNA gene amplicon sequences revealed that the bacterial community comprises Nitrospirae (47%), “Parcubacteria” (19%), Deinococcus-Thermus (16%), and Actinobacteria (9%), among others. Notably, only 57 amplicon sequence variants (ASV) were detected, and fifteen of these accounted for 90% of the amplicons. Among the abundant ASVs, an early-branching, uncultivated actinobacterial clade identified as RBG-16-55-12 in the SILVA database was detected. Ten single-cell genomes (average pairwise nucleotide identity: 0.98–1.00; estimated completeness: 33–93%; estimated genome size: ~2.3 Mb) that affiliated with this clade were obtained. Taxonomic classification using single copy genes indicates that the genomes belong to the actinobacterial class-level clade UBA1414 in the Genome Taxonomy Database. Based on metabolic pathway predictions, these actinobacteria are anaerobes, capable of glycolysis, dissimilatory nitrate reduction and CO 2 fixation via the Wood–Ljungdahl (WL) pathway. Several other genomes within UBA1414 and two related class-level clades also encode the WL pathway, which has not yet been reported for the Actinobacteria phylum. For the Hakuba actinobacterium, the energy metabolism related to the WL pathway is likely supported by a combination of the Rnf complex, group 3b and 3d [NiFe]-hydrogenases, [FeFe]-hydrogenases, and V-type (H + /Na + pump) ATPase. The genomes also harbor a form IV ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) complex, also known as a RubisCO-like protein, and contain signatures of interactions with viruses, including clustered regularly interspaced short palindromic repeat (CRISPR) regions and several phage integrases. This is the first report and detailed genome analysis of a bacterium within the Actinobacteria phylum capable of utilizing the WL pathway. The Hakuba actinobacterium is a member of the clade UBA1414/RBG-16-55-12, formerly within the group “OPB41.” We propose to name this bacterium ‘Candidatus Hakubanella thermoalkaliphilus.'
Microbially induced calcite precipitation (MICP) is an alternative to existing soil stabilization techniques for construction and erosion. As with any biologically induced process in soils or aquifers, it is important to track changes in the microbial communities that occur as a result of the treatment. Our research assessed how native microbial communities developed in response to injections of reactants (dilute molasses as a carbon source; urea as a source of nitrogen and alkalinity) that promoted MICP in a shallow aquifer. Microbial community composition (16S rRNA gene) and ureolytic potential (ureC gene copy numbers) were also measured in groundwater and artificial sediment. Aquifer geochemistry showed evidence of sulfate reduction, nitrification, denitrification, ureolysis, and iron reduction during the treatment. The observed changes in geochemistry corresponded to microbial community succession in the groundwater and this matched parallel geophysical and mineralogical evidence of calcite precipitation in the aquifer. We detected an increase in the number of ureC genes in the microbial communities at the end of the injection period, suggesting an increase in the abundance of microbes possessing this gene as needed to hydrolyze urea and stimulate MICP. We identify geochemical and biological markers that highlight the microbial community response that can be used along with geophysical and geotechnical evidence to assess progress of MICP.
Microorganisms have evolved several mechanisms to mobilize and mineralize occluded and insoluble phosphorus (P), thereby promoting plant growth in terrestrial ecosystems. However, the linkages between microbial P-solubilization traits and the preponderance of insoluble P in natural ecosystems are not well known. We tested the P solubilization traits of hundreds of culturable bacteria representative of the rhizosphere from a natural gradient where P concentration and bioavailability decline as soil becomes progressively more weathered. Aluminum, iron phosphate and organic P (phytate) were expected to dominate in more weathered soils. A defined cultivation medium with these chemical forms of P was used for isolation. A combination of soil chemical, spectroscopic analyses and 16S rRNA gene sequencing were used to understand the in situ ability for solubilization of these predominant forms of P. Locations with more occluded and organic P harbored the greatest abundance of P-mobilizing microorganisms, especially Burkholderiaceae ( Caballeronia and Paraburkholderia spp.). Nearly all bacteria utilized aluminum phosphate, however fewer could subsist on iron phosphate (FePO 4 ) or phytate. Microorganisms isolated from phytic acid were also most effective at solubilizing FePO 4 , suggesting that phytate solubilization may be linked to the ability to solubilize Fe. Significantly, we observed Fe to be co-located with P in organic patches in soil. Siderophore addition in lab experiments reinstated phytase mediated P-solubilization from Fe-phytate complexes. Taken together, these results indicate that metal-organic-P complex formation may limit enzymatic P solubilization from phytate in soil. Additionally, the linked traits of phytase and siderophore production were mostly restricted to specific clades within the Burkholderiaceae . We propose that Fe complexation of organic P (e.g., phytate) represents a major constraint on P turnover and availability in acidic soils, as only a limited subset of bacteria appear to possess the traits required to access this persistent pool of soil P.
Taxonomic decisions within the order Rhizobiales have relied heavily on the interpretations of highly conserved 16S rRNA sequences and DNA–DNA hybridizations (DDH). Currently, bacterial species are defined as including strains that present 95–96% of average nucleotide identity (ANI) and 70% of digital DDH (dDDH). Thus, ANI values from 520 genome sequences of type strains from species of Rhizobiales order were computed. From the resulting 270,400 comparisons, a ≥95% cut-off was used to extract high identity genome clusters through enumerating maximal cliques. Coupling this graph-based approach with dDDH from clusters of interest, it was found that: (i) there are synonymy between Aminobacter lissarensis and Aminobacter carboxidus, Aurantimonas manganoxydans and Aurantimonas coralicida, “Bartonella mastomydis,” and Bartonella elizabethae, Chelativorans oligotrophicus, and Chelativorans multitrophicus, Rhizobium azibense, and Rhizobium gallicum, Rhizobium fabae, and Rhizobium pisi, and Rhodoplanes piscinae and Rhodoplanes serenus; (ii) Chelatobacter heintzii is not a synonym of Aminobacter aminovorans; (iii) “Bartonella vinsonii” subsp. arupensis and “B. vinsonii” subsp. berkhoffii represent members of different species; (iv) the genome accessions GCF_003024615.1 (“Mesorhizobium loti LMG 6125T”), GCF_003024595.1 (“Mesorhizobium plurifarium LMG 11892T”), GCF_003096615.1 (“Methylobacterium organophilum DSM 760T”), and GCF_000373025.1 (“R. gallicum R-602 spT”) are not from the genuine type strains used for the respective species descriptions; and v) “Xanthobacter autotrophicus” Py2 and “Aminobacter aminovorans” KCTC 2477T represent cases of misuse of the term “type strain”. Aminobacter heintzii comb. nov. and the reclassification of Aminobacter ciceronei as A. heintzii is also proposed. To facilitate the downstream analysis of large ANI matrices, we introduce here ProKlust (“Prokaryotic Clusters”), an R package that uses a graph-based approach to obtain, filter, and visualize clusters on identity/similarity matrices, with settable cut-off points and the possibility of multiple matrices entries.
The conversion of mercury (Hg) to monomethylmercury (MMHg) is a critical area of concern in global Hg cycling. Periphyton biofilms may harbor significant amounts of MMHg but little is known about the Hg-methylating potential of the periphyton microbiome. Therefore, we used high-throughput amplicon sequencing of the 16S rRNA gene, ITS2 region, and Hg methylation gene pair (hgcAB) to characterize the archaea/bacteria, fungi, and Hg-methylating microorganisms in periphyton communities grown in a contaminated watershed in East Tennes(see United States). Furthermore, we examined how nutrient amendments (nitrate and/or phosphate) altered periphyton community structure and function. We found that bacterial/archaeal richness in experimental conditions decreased in summer and increased in autumn relative to control treatments, while fungal diversity generally increased in summer and decreased in autumn relative to control treatments. Interestingly, the Hg-methylating communities were dominated by Proteobacteria followed by Candidatus Atribacteria across both seasons. Surprisingly, Hg methylation potential correlated with numerous bacterial families that do not contain hgcAB, suggesting that the overall microbiome structure of periphyton communities influences rates of Hg transformation within these microbial mats. To further explore these complex community interactions, we performed a microbial network analysis and found that the nitrate-amended treatment resulted in the highest number of hub taxa that also corresponded with enhanced Hg methylation potential. This work provides insight into community interactions within the periphyton microbiome that may contribute to Hg cycling and will inform future research that will focus on establishing mixed microbial consortia to uncover mechanisms driving shifts in Hg cycling within periphyton habitats.
Dryland ecosystems are sensitive to perturbations and generally slow to recover post disturbance. The microorganisms residing in dryland soils are especially important as they contribute to soil structure and nutrient cycling. Disturbance can have particularly strong effects on dryland soil structure and function, yet the natural resistance and recovery of the microbial components of dryland soils has not been well documented. In this study, the recovery of surface soil bacterial communities from multiple physical and environmental disturbances is assessed. Samples were collected from three field sites in the vicinity of Moab, UT, United States, 6 to 7 years after physical and climate disturbance manipulations had been terminated, allowing for the assessment of community recovery. Additionally, samples were collected in a transect that included three habitat patches: the canopy zone soils under the dominant shrubs, the interspace soils that are colonized by biological soil crusts, and edge soils at the plot borders. Field site and habitat patch were significant factors structuring the bacterial communities, illustrating that sites and habitats harbored unique soil microbiomes. Across the different sites and disturbance treatments, there was evidence of significant bacterial community recovery, as bacterial biomass and diversity were not significantly different than control plots. There was, however, a small number of 16S rRNA gene amplicon sequence variants that distinguished particular treatments, suggesting that legacy effects of the disturbances still remained. Taken together, these data suggest that dryland bacterial communities may possess a previously unappreciated potential to recover within years of the original disturbance.
Bioenergy crops are a promising energy alternative to fossil fuels. During bioenergy feedstock production, crop inputs shape the composition of soil microbial communities, which in turn influences nutrient cycling and plant productivity. In addition to cropping inputs, site characteristics (e.g., soil texture, climate) influence bacterial and fungal communities. We explored the response of soil microorganisms to bioenergy cropping system (switchgrass vs. maize) and site (sandy loam vs. silty loam) within two long-term experimental research stations. The live and total microbial community membership was investigated using 16S and ITS amplicon sequencing of soil RNA and DNA. For both nucleic acid types, we expected fungi and prokaryotes to be differentially impacted by crop and site due their dissimilar life strategies. We also expected live communities to be more strongly affected by site and crop than the total communities due to a sensitivity to recent stimuli. Instead, we found that prokaryotic and fungal community composition was primarily driven by site with a secondary crop effect, highlighting the importance of soil texture and fertility in shaping both communities. Specific highly abundant prokaryotic and fungal taxa within live communities were indicative of site and cropping systems, providing insight into treatment-specific, agriculturally relevant microbial taxa that were obscured within total community profiles. Within live prokaryote communities, predatory Myxobacteria spp. were largely indicative of silty and switchgrass communities. Within live fungal communities, Glomeromycota spp. were solely indicative of switchgrass soils, while a few very abundant Mortierellomycota spp. were indicative of silty soils. Site and cropping system had distinct effects on the live and total communities reflecting selection forces of plant inputs and environmental conditions over time. Comparisons between RNA and DNA communities uncovered live members obscured within the total community as well as members of the relic DNA pool. The associations between live communities and relic DNA are a product of the intimate relationship between the ephemeral responses of the live community and the accumulation of DNA within necromass that contributes to soil organic matter, and in turn shapes soil microbial dynamics.
Introduction Bodies recovered from water, especially in the late phase of decomposition, pose difficulties to the investigating authorities. Various methods have been proposed for postmortem submersion interval (PMSI) estimation and drowning identification, but some limitations remain. Many recent studies have proved the value of microbiota succession in viscera for postmortem interval estimation. Nevertheless, the visceral microbiota succession and its application for PMSI estimation and drowning identification require further investigation. Methods In the current study, mouse drowning and CO 2 asphyxia models were developed, and cadavers were immersed in freshwater for 0 to 14 days. Microbial communities in the liver and brain were characterized via 16S rDNA high-throughput sequencing. Results Only livers and brains collected from 5 to 14 days postmortem were qualified for sequencing. There was significant variation between microbiota from liver and brain. Differences in microbiota between the cadavers of mice that had drowned and those only subjected to postmortem submersion decreased over the PMSI. Significant successions in microbial communities were observed among the different subgroups within the late phase of the PMSI in livers and brains. Eighteen taxa in the liver which were mainly related to Clostridium_sensu_stricto and Aeromonas , and 26 taxa in the brain which were mainly belonged to Clostridium_sensu_stricto , Acetobacteroides , and Limnochorda , were selected as potential biomarkers for PMSI estimation based on a random forest algorithm. The PMSI estimation models established yielded accurate prediction results with mean absolute errors ± the standard error of 1.282 ± 0.189 d for the liver and 0.989 ± 0.237 d for the brain. Conclusions The present study provides novel information on visceral postmortem microbiota succession in corpses submerged in freshwater which sheds new light on PMSI estimation based on the liver and brain in forensic practice.
There are some limitations of traditional influenza vaccines concerning novel mutant strains. Therefore, it is particularly important to develop preventive means for antigen-unrelated types of influenza viruses. Recent studies have shown that probiotics can modulate the immune system and reduce the severity of viral infections. In this study, we investigated the potential of Lactiplantibacillus plantarum 0111 against influenza virus H9N2. Challenge experiments showed that L. plantarum 0111 pretreatments could effectively improve mice’s survival rate and weight loss and reduce the inflammatory cytokines IL-6 and TNF-α in the lungs and bronchoalveolar lavage fluid (BALF) along with the degree of lung and intestinal injury. FMT experiment demonstrates that the protective effect produced by L. plantarum 0111 is associated with gut microorganisms. In addition, 16S high-throughput sequencing of the mouse intestinal microbiota showed that L. plantarum 0111 remodeled the intestinal microbiota after H9N2 infection and maintained the gut microbiota balance. In a mouse model, the oral administration of L. plantarum 0111 increased IFN-β expression in the serum and BALF. At the same time, the transcript levels of IFN-β and related ISGs in the intestine and lungs of mice were also increased. In addition, the activation and polarization of T cells in mesenteric lymph nodes (MLNs) and the spleen were detected by flow cytometry, and the results showed that L. plantarum 0111 modulated cytokines in T cells and increased IgA expression in B cells in the MLNs and spleen. Thus, L. plantarum 0111 may improve gut microbiota-mediated immune responses and thus, resist infection by the influenza virus, and it could be used as an effective preventive measure against the influenza virus.
As marine sediments are buried, microbial communities transition from sulfate-reduction to methane-production after sulfate is depleted. When this biogenic methane diffuses into the overlying sulfate-rich sediments, it forms a sulfate-methane transition zone (SMTZ) because sulfate reducers deplete hydrogen concentrations and make hydrogenotrophic methanogenesis exergonic in the reverse direction, a process called the anaerobic oxidation of methane (AOM). Microbial participation in these processes is often inferred from geochemistry, genes, and gene expression changes with sediment depth, using sedimentation rates to convert depth to time. Less is known about how natural sediments transition through these geochemical states transition in real-time. We examined 16S rRNA gene amplicon libraries and metatranscriptomes in microcosms of anoxic sediment from the White Oak River estuary, NC, with three destructively sampled replicates with methane added (586-day incubations) and three re-sampled un-amended replicates (895-day incubations). Sulfate dropped to a low value (∼0.3 mM) on similar days for both experiments (312 and 320 days, respectively), followed by a peak in hydrogen, intermittent increases in methane-cycling archaea starting on days 375 and 362 (mostly Methanolinea spp. and Methanosaeta spp., and Methanococcoides sp. ANME-3), and a methane peak 1 month later. However, methane δ 13 C values only show net methanogenesis 6 months after methane-cycling archaea increase and 4 months after the methane peak, when sulfate is consistently below 0.1 mM and hydrogen increases to a stable 0.61 ± 0.13 nM (days 553–586, n = 9). Sulfate-reducing bacteria (mostly Desulfatiglans spp. and Desulfosarcina sp. SEEP-SRB1) increase in relative abundance only during this period of net methane production, suggesting syntrophy with methanogens in the absence of sulfate. The transition from sulfate reduction to methane production in marine sediments occurs through a prolonged period of methane-cycling by methanogens at low sulfate concentrations, and steady growth of sulfate reducers along with methanogens after sulfate is depleted.