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1. Metagenomic profiles of archaea and bacteria within thermal and geochemical gradients of the Guaymas Basin deep subsurface

   https://doi.org/10.1038/s41467-023-43296-x  

   Mara, Paraskevi; Geller-McGrath, David; Edgcomb, Virginia; Beaudoin, David; Morono, Yuki; Teske, Andreas (November 2023, Nature Communications)

   Abstract Previous studies of microbial communities in subseafloor sediments reported that microbial abundance and diversity decrease with sediment depth and age, and microbes dominating at depth tend to be a subset of the local seafloor community. However, the existence of geographically widespread, subsurface-adapted specialists is also possible. Here, we use metagenomic and metatranscriptomic analyses of the hydrothermally heated, sediment layers of Guaymas Basin (Gulf of California, Mexico) to examine the distribution and activity patterns of bacteria and archaea along thermal, geochemical and cell count gradients. We find that the composition and distribution of metagenome-assembled genomes (MAGs), dominated by numerous lineages of Chloroflexota and Thermoproteota, correlate with biogeochemical parameters as long as temperatures remain moderate, but downcore increasing temperatures beyond ca. 45 ºC override other factors. Consistently, MAG size and diversity decrease with increasing temperature, indicating a downcore winnowing of the subsurface biosphere. By contrast, specific archaeal MAGs within the Thermoproteota and Hadarchaeota increase in relative abundance and in recruitment of transcriptome reads towards deeper, hotter sediments, marking the transition towards a specialized deep, hot biosphere. 

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2. Data report: the DNA event horizon in the Guaymas Basin subsurface biosphere: technical advances and redefined limits in bulk extractions of nucleic acids from deep marine sediments, IODP Expedition 385

   https://doi.org/10.14379/iodp.proc.385.204.2024  

   Ramírez, GA; Mara, P; Beaudoin, D; Bojanova, D; Hinkle, JE; Kingham, B; Edgcomb, VP; Morono, Y; Teske, A (October 2024, Proceedings of the International Ocean Discovery Program Expedition reports)

   We compiled DNA and RNA isolation protocols for sediment bulk extraction and their yields from Guaymas Basin subsurface sediments recovered during International Ocean Discovery Program Expedition 385 and evaluated their sensitivity for metagenomic and amplicon analyses of subsurface microbial communities. Guaymas Basin sediments present a challenge for DNA and RNA recovery due to high concentrations of hydrocarbons, steep thermal gradients, and rapidly declining cell numbers downhole. Metagenomic library construction and sequencing was possible from as little as 0.2 to 0.5 ng DNA/cm3 sediment; polymerase chain reaction (PCR) amplification of 16S rRNA genes required in most cases approximately 1–2 ng DNA/cm3 sediment. At in situ temperatures of 50° to 60°C, decreasing DNA recovery leads to increasingly uncertain hit or miss outcomes and failures for metagenomic and amplicon analyses. DNA concentration profiles show that, even before these hot temperatures are reached, relatively moderate temperatures (near 40°C) have a major effect on microbial abundance and DNA yield. Comparison with cell count profiles shows that hydrothermal influence reduces downhole cell densities by multiple orders of magnitude compared to nonhydrothermal sediments. This effect is also visible at relatively moderate temperatures. RNA recovery is highly sensitive to downhole increasing temperatures and decreasing cell numbers, and was most efficient for microbial communities in cool, relatively shallow subsurface sediments. 

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3. Influence of Seasonal Succession on Microbiological and Physiochemical Composition in Shallow Estuarine Sediments

   https://doi.org/10.1111/1462-2920.70194  

   Bowen, Malique R; Agblemanyo, Felix E; Persad, Porscha M; Wozniak, Andrew S; Biddle, Jennifer F (October 2025, Environmental Microbiology)

   ABSTRACT Marine sediments harbour diverse microbial populations, but with increasing depth, these microbes are thought to have low activity due to depleted electron acceptors and lack of new organic matter after burial. However, physiochemical changes in environmental parameters could impact the metabolic activity of microbes in marine sediments. We performed seasonal sampling of shallow sediments to examine changes in population and abundance in relation to physiochemical changes over the year. We used amplicon sequencing, quantitative PCR and geochemistry to assess seasonal abundance of microbial populations at 3 depths (12–14, 38–40 and 48–50 cm) in shallow coastal sediments. 16S rRNA amplicon sequencing showed the sediment microbiome consists of common sediment taxa with minor seasonal variation. However, bacterial gene counts of 16S rRNA genes were highest in summer (2.50 × 10¹² genes/g of sediment) and lowest in spring (1.64 × 10¹¹ genes/g sediment). We observed differences in sediment temperature at depth across seasons (Summer 28°C–25.5°C; Winter 8.7°C–6.3°C) and correlated changes in dissolved organic matter composition that are not typically reported for this environment. We conclude deeper microbial populations in shallow sediments may experience seasonal abundance shifts resulting in a more variable subsurface community than initially presumed in the literature. 

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4. Well-hidden methanogenesis in deep, organic-rich sediments of Guaymas Basin

   https://doi.org/10.1038/s41396-023-01485-y  

   Bojanova, Diana P.; De Anda, Valerie Y.; Haghnegahdar, Mojhgan A.; Teske, Andreas P.; Ash, Jeanine L.; Young, Edward D.; Baker, Brett J.; LaRowe, Douglas E.; Amend, Jan P. (August 2023, The ISME Journal)

   Abstract Deep marine sediments (>1mbsf) harbor ~26% of microbial biomass and are the largest reservoir of methane on Earth. Yet, the deep subsurface biosphere and controls on its contribution to methane production remain underexplored. Here, we use a multidisciplinary approach to examine methanogenesis in sediments (down to 295 mbsf) from sites with varying degrees of thermal alteration (none, past, current) at Guaymas Basin (Gulf of California) for the first time. Traditional (13C/12C and D/H) and multiply substituted (13CH3D and 12CH2D2) methane isotope measurements reveal significant proportions of microbial methane at all sites, with the largest signal at the site with past alteration. With depth, relative microbial methane decreases at differing rates between sites. Gibbs energy calculations confirm methanogenesis is exergonic in Guaymas sediments, with methylotrophic pathways consistently yielding more energy than the canonical hydrogenotrophic and acetoclastic pathways. Yet, metagenomic sequencing and cultivation attempts indicate that methanogens are present in low abundance. We find only one methyl-coenzyme M (mcrA) sequence within the entire sequencing dataset. Also, we identify a wide diversity of methyltransferases (mtaB, mttB), but only a few sequences phylogenetically cluster with methylotrophic methanogens. Our results suggest that the microbial methane in the Guaymas subsurface was produced over geologic time by relatively small methanogen populations, which have been variably influenced by thermal sediment alteration. Higher resolution metagenomic sampling may clarify the modern methanogen community. This study highlights the importance of using a multidisciplinary approach to capture microbial influences in dynamic, deep subsurface settings like Guaymas Basin. 

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5. Potential for microbial denitrification coupled with methanol oxidation found in abundant MAGs in Antarctic Peninsula sediments

   Howland, KE; Nygaard, HJ; Steen, AD; Halanych, KM; Mahon, AR; Learman, DR (May 2025, FEMS microbiology letters)

   Denitrification accounts for a substantial nitrogen loss from environmental systems, shifting microbial composition and impacting other biogeochemical cycles. In Antarctica, rising temperatures cause increased organic matter deposition in marine sediments, which can significantly alter microbially mediated denitrification. To examine the genetic potential of microorganisms driving N-cycling in these sediments, benthic sediment cores were collected at two sites in the Weddell Sea, Antarctica. DNA was extracted from multiple depths at each site, resulting in the reconstruction of 75 high-quality metagenome-assembled genomes (MAGs). Forty-seven of these MAGs contained reductases involved in denitrification. MAGs belonging to the genus Methyloceanibacter were the most abundant MAGs at both sites and all depths, except depth 3–6 cmbsf at one site, where they were not identified. The abundance of these Methyloceanibacter MAGs suggests the potential for nitrate-driven methanol oxidation at both sites. MAGs belonging to Beggiatoaceae and Sedimenticolaceae were found to have the genetic potential to produce intermediates in denitrification and the complete pathway for dissimilatory nitrate reduction to ammonia. MAGs within Acidimicrobiia and Dadabacteria had the potential to complete the final denitrification step. Based on MAGs, Antarctic peninsula sediment communities have the potential for complete denitrification and dissimilatory nitrate reduction to ammonia via a consortium. 

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