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1. Climate drivers alter nitrogen availability in surface peat and decouple N2 fixation from CH4 oxidation in the Sphagnum moss microbiome

   https://doi.org/10.1111/gcb.16651  

   Petro, Caitlin ; Carrell, Alyssa A. ; Wilson, Rachel M. ; Duchesneau, Katherine ; Noble‐Kuchera, Sekou ; Song, Tianze ; Iversen, Colleen M. ; Childs, Joanne ; Schwaner, Geoff ; Chanton, Jeffrey P. ; et al ( March 2023 , Global Change Biology)

   Peat mosses (Sphagnumspp.) are keystone species in boreal peatlands, where they dominate net primary productivity and facilitate the accumulation of carbon in thick peat deposits.Sphagnummosses harbor a diverse assemblage of microbial partners, including N₂‐fixing (diazotrophic) and CH₄‐oxidizing (methanotrophic) taxa that support ecosystem function by regulating transformations of carbon and nitrogen. Here, we investigate the response of theSphagnumphytobiome (plant + constituent microbiome + environment) to a gradient of experimental warming (+0°C to +9°C) and elevated CO₂(+500 ppm) in an ombrotrophic peatland in northern Minnesota (USA). By tracking changes in carbon (CH₄, CO₂) and nitrogen (NH₄‐N) cycling from the belowground environment up toSphagnumand its associated microbiome, we identified a series of cascading impacts to theSphagnumphytobiome triggered by warming and elevated CO₂. Under ambient CO₂, warming increased plant‐available NH₄‐N in surface peat, excess N accumulated inSphagnumtissue, and N₂fixation activity decreased. Elevated CO₂offset the effects of warming, disrupting the accumulation of N in peat andSphagnumtissue. Methane concentrations in porewater increased with warming irrespective of CO₂treatment, resulting in a ~10× rise in methanotrophic activity withinSphagnumfrom the +9°C enclosures. Warming's divergent impacts on diazotrophy and methanotrophy caused these processes to become decoupled at warmer temperatures, as evidenced by declining rates of methane‐induced N₂fixation and significant losses of keystone microbial taxa. In addition to changes in theSphagnummicrobiome, we observed ~94% mortality ofSphagnumbetween the +0°C and +9°C treatments, possibly due to the interactive effects of warming on N‐availability and competition from vascular plant species. Collectively, these results highlight the vulnerability of theSphagnumphytobiome to rising temperatures and atmospheric CO₂concentrations, with significant implications for carbon and nitrogen cycling in boreal peatlands.

    

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2. Experimentally-validated correlation analysis reveals new anaerobic methane oxidation partnerships with consortium-level heterogeneity in diazotrophy

   https://doi.org/10.1038/s41396-020-00757-1  

   Metcalfe, Kyle S. ; Murali, Ranjani ; Mullin, Sean W. ; Connon, Stephanie A. ; Orphan, Victoria J. ( October 2020 , The ISME Journal)

   Archaeal anaerobic methanotrophs (“ANME”) and sulfate-reducing Deltaproteobacteria (“SRB”) form symbiotic multicellular consortia capable of anaerobic methane oxidation (AOM), and in so doing modulate methane flux from marine sediments. The specificity with which ANME associate with particular SRB partners in situ, however, is poorly understood. To characterize partnership specificity in ANME-SRB consortia, we applied the correlation inference technique SparCC to 310 16S rRNA amplicon libraries prepared from Costa Rica seep sediment samples, uncovering a strong positive correlation between ANME-2b and members of a clade of Deltaproteobacteria we termed SEEP-SRB1g. We confirmed this association by examining 16S rRNA diversity in individual ANME-SRB consortia sorted using flow cytometry and by imaging ANME-SRB consortia with fluorescence in situ hybridization (FISH) microscopy using newly-designed probes targeting the SEEP-SRB1g clade. Analysis of genome bins belonging to SEEP-SRB1g revealed the presence of a complete nifHDK operon required for diazotrophy, unusual in published genomes of ANME-associated SRB. Active expression of nifH in SEEP-SRB1g within ANME-2b—SEEP-SRB1g consortia was then demonstrated by microscopy using hybridization chain reaction (HCR-) FISH targeting nifH transcripts and diazotrophic activity was documented by FISH-nanoSIMS experiments. NanoSIMS analysis of ANME-2b—SEEP-SRB1g consortia incubated with a headspace containing CH4 and 15N2 revealed differences in cellular 15N-enrichment between the two partners that varied between individual consortia, with SEEP-SRB1g cells enriched in 15N relative to ANME-2b in one consortium and the opposite pattern observed in others, indicating both ANME-2b and SEEP-SRB1g are capable of nitrogen fixation, but with consortium-specific variation in whether the archaea or bacterial partner is the dominant diazotroph.

    

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3. Community structure of coral microbiomes is dependent on host morphology

   https://doi.org/10.1186/s40168-022-01308-w  

   Morrow, Kathleen M. ; Pankey, M. Sabrina ; Lesser, Michael P. ( December 2022 , Microbiome)

   Abstract Background The importance of symbiosis has long been recognized on coral reefs, where the photosynthetic dinoflagellates of corals (Symbiodiniaceae) are the primary symbiont. Numerous studies have now shown that a diverse assemblage of prokaryotes also make-up part of the microbiome of corals. A subset of these prokaryotes is capable of fixing nitrogen, known as diazotrophs, and is also present in the microbiome of scleractinian corals where they have been shown to supplement the holobiont nitrogen budget. Here, an analysis of the microbiomes of 16 coral species collected from Australia, Curaçao, and Hawai’i using three different marker genes (16S rRNA, nif H, and ITS2) is presented. These data were used to examine the effects of biogeography, coral traits, and ecological life history characteristics on the composition and diversity of the microbiome in corals and their diazotrophic communities. Results The prokaryotic microbiome community composition (i.e., beta diversity) based on the 16S rRNA gene varied between sites and ecological life history characteristics, but coral morphology was the most significant factor affecting the microbiome of the corals studied. For 15 of the corals studied, only two species Pocillopora acuta and Seriotopora hystrix , both brooders, showed a weak relationship between the 16S rRNA gene community structure and the diazotrophic members of the microbiome using the nif H marker gene, suggesting that many corals support a microbiome with diazotrophic capabilities. The order Rhizobiales , a taxon that contains primarily diazotrophs, are common members of the coral microbiome and were eight times greater in relative abundances in Hawai’i compared to corals from either Curacao or Australia. However, for the diazotrophic component of the coral microbiome, only host species significantly influenced the composition and diversity of the community. Conclusions The roles and interactions between members of the coral holobiont are still not well understood, especially critical functions provided by the coral microbiome (e.g., nitrogen fixation), and the variation of these functions across species. The findings presented here show the significant effect of morphology, a coral “super trait,” on the overall community structure of the microbiome in corals and that there is a strong association of the diazotrophic community within the microbiome of corals. However, the underlying coral traits linking the effects of host species on diazotrophic communities remain unknown. 

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4. Abundance, Identity, and Potential Diazotrophic Activity of nifH ‐Containing Organisms at Marine Cold Seeps

   https://doi.org/10.1111/1462-2920.70058  

   Semler, Amanda_C ; Paris, Emily_R ; Salvador, Mikaela ; Dekas, Anne_E ( March 2025 , Environmental Microbiology)

   Diazotrophic microorganisms alleviate nitrogen limitation at marine cold seeps using nitrogenase, encoded in part by the genenifH. Here, we investigatednifH‐containing organisms (NCOs) inside and outside six biogeochemically heterogeneous seeps using amplicon sequencing and quantitative real‐time PCR (qPCR) ofnifHgenes and transcripts. We detectednifHgenes affiliated with phylogenetically and metabolically diverse organisms spanning 18 bacterial and archaeal phyla (17 within seeps). Detected NCOs included methane‐oxidising ANME‐2 archaea and sulfate‐reducing Desulfobacteraceae, which have been shown to fix nitrogen at seeps previously, as well as Desulfuromonadales and putatively hydrocarbon‐oxidisingDesulfoglaebaandCandidatusMethanoliparia. We detectednifHtranscripts at five of the six seeps, suggesting widespread diazotrophic activity. We corrected our qPCR data based on our amplicon results, which found that 71% of recovered sequences were not bona fidenifH,and we recommend a similar correction in future qPCR studies that use broadnifHprimers.NifHabundance was up to three orders of magnitude higher within seeps, was correlated withmcrAabundance, and, when corrected, was negatively correlated with porewater ammonium < 25 μM, consistent with the inhibition of diazotrophy by ammonium. Our findings expand the known diversity of NCOs at seeps and emphasise seeps as hotspots for deep‐sea diazotrophy.

    

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5. Widespread nitrogen fixation in sediments from diverse deep‐sea sites of elevated carbon loading

   https://doi.org/10.1111/1462-2920.14342  

   Dekas, Anne E. ; Fike, David A. ; Chadwick, Grayson L. ; Green‐Saxena, Abigail ; Fortney, Julian ; Connon, Stephanie A. ; Dawson, Katherine S. ; Orphan, Victoria J. ( July 2018 , Environmental Microbiology)

   Nitrogen fixation, the biological conversion of N₂to NH₃, is critical to alleviating nitrogen limitation in many marine ecosystems. To date, few measurements exist of N₂fixation in deep‐sea sediments. Here, we conducted > 400 bottle incubations with sediments from methane seeps, whale falls and background sites off the western coast of the United States from 600 to 2893 m water depth to investigate the potential rates, spatial distribution and biological mediators of benthic N₂fixation. We found that N₂fixation was widespread, yet heterogeneously distributed with sediment depth at all sites. In some locations, rates exceeded previous measurements by > 10×, and provided up to 30% of the community anabolic growth requirement for nitrogen. Diazotrophic activity appeared to be inhibited by pore water ammonium: N₂fixation was only observed if incubation ammonium concentrations were ≤ 25 μM, and experimental additions of ammonium reduced diazotrophy. In seep sediments, N₂fixation was dependent on CH₄and coincident with sulphate reduction, consistent with previous work showing diazotrophy by microorganisms mediating sulphate‐coupled methane oxidation. However, the pattern of diazotrophy was different in whale‐fall and associated reference sediments, where it was largely unaffected by CH₄, suggesting catabolically different diazotrophs at these sites.

    

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