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1. Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments

   https://doi.org/s41467-018-07418-0  

   Nina Dombrowski, Andreas P. (November 2018, Nature communications)

   Microbes in Guaymas Basin (Gulf of California) hydrothermal sediments thrive on hydrocarbons and sulfur and experience steep, fluctuating temperature and chemical gradients. The functional capacities of communities inhabiting this dynamic habitat are largely unknown. Here, we reconstructed 551 genomes from hydrothermally influenced, and nearby cold sediments belonging to 56 phyla (40 uncultured). These genomes comprise 22 unique lineages, including five new candidate phyla. In contrast to findings from cold hydrocarbon seeps, hydrothermal-associated communities are more diverse and archaea dominate over bacteria. Genome-based metabolic inferences provide first insights into the ecological niches of these uncultured microbes, including methane cycling in new Crenarchaeota and alkane utilization in ANME-1. These communities are shaped by a high biodiversity, partitioning among nitrogen and sulfur pathways and redundancy in core carbon-processing pathways. The dynamic sediments select for distinctive microbial communities that stand out by expansive biodiversity, and open up new physiological perspectives into hydrothermal ecosystem function. 

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2. Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups

   https://doi.org/10.1038/s41396-021-01057-y  

   Langwig, Marguerite V.; De Anda, Valerie; Dombrowski, Nina; Seitz, Kiley W.; Rambo, Ian M.; Greening, Chris; Teske, Andreas P.; Baker, Brett J. (July 2021, The ISME Journal)

   Abstract Deltaproteobacteria, now proposed to be the phyla Desulfobacterota, Myxococcota, and SAR324, are ubiquitous in marine environments and play essential roles in global carbon, sulfur, and nutrient cycling. Despite their importance, our understanding of these bacteria is biased towards cultured organisms. Here we address this gap by compiling a genomic catalog of 1 792 genomes, including 402 newly reconstructed and characterized metagenome-assembled genomes (MAGs) from coastal and deep-sea sediments. Phylogenomic analyses reveal that many of these novel MAGs are uncultured representatives of Myxococcota and Desulfobacterota that are understudied. To better characterize Deltaproteobacteria diversity, metabolism, and ecology, we clustered ~1 500 genomes based on the presence/absence patterns of their protein families. Protein content analysis coupled with large-scale metabolic reconstructions separates eight genomic clusters of Deltaproteobacteria with unique metabolic profiles. While these eight clusters largely correspond to phylogeny, there are exceptions where more distantly related organisms appear to have similar ecological roles and closely related organisms have distinct protein content. Our analyses have identified previously unrecognized roles in the cycling of methylamines and denitrification among uncultured Deltaproteobacteria. This new view of Deltaproteobacteria diversity expands our understanding of these dominant bacteria and highlights metabolic abilities across diverse taxa. 

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3. Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean

   https://doi.org/10.1128/msystems.00619-23  

   Vázquez Rosas Landa, Mirna; De Anda, Valerie; Rohwer, Robin R.; Angelova, Angelina; Waldram, Georgia; Gutierrez, Tony; Baker, Brett J. (September 2023, mSystems)

   Mackelprang, Rachel (Ed.)

   Petroleum pollution in the ocean has increased because of rapid population growth and modernization, requiring urgent remediation. Our understanding of the metabolic response of native microbial communities to oil spills is not well understood. Here, we explored the baseline hydrocarbon-degrading communities of a subarctic Atlantic region to uncover the metabolic potential of the bacteria that inhabit the surface and subsurface water. We conducted enrichments with a 13 C-labeled hydrocarbon to capture the fraction of the community actively using the hydrocarbon. We then combined this approach with metagenomics to identify the metabolic potential of this hydrocarbon-degrading community. This revealed previously undescribed uncultured bacteria with unique metabolic mechanisms involved in aerobic hydrocarbon degradation, indicating that temperature may be pivotal in structuring hydrocarbon-degrading baseline communities. Our findings highlight gaps in our understanding of the metabolic complexity of hydrocarbon degradation by native marine microbial communities. 

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4. Activity-based cell sorting reveals responses of uncultured archaea and bacteria to substrate amendment

   https://doi.org/10.1038/s41396-020-00749-1  

   Reichart, Nicholas J.; Jay, Zackary J.; Krukenberg, Viola; Parker, Albert E.; Spietz, Rachel L.; Hatzenpichler, Roland (September 2020, The ISME Journal)

   Abstract Metagenomic studies have revolutionized our understanding of the metabolic potential of uncultured microorganisms in various ecosystems. However, many of these genomic predictions have yet to be experimentally tested, and the functional expression of genomic potential often remains unaddressed. In order to obtain a more thorough understanding of cell physiology, novel techniques capable of testing microbial metabolism under close to in situ conditions must be developed. Here, we provide a benchmark study to demonstrate that bioorthogonal non-canonical amino acid tagging (BONCAT) in combination with fluorescence-activated cell sorting (FACS) and 16S rRNA gene sequencing can be used to identify anabolically active members of a microbial community incubated in the presence of various growth substrates or under changing physicochemical conditions. We applied this approach to a hot spring sediment microbiome from Yellowstone National Park (Wyoming, USA) and identified several microbes that changed their activity levels in response to substrate addition, including uncultured members of the phyla Thaumarchaeota, Acidobacteria, and Fervidibacteria. Because shifts in activity in response to substrate amendment or headspace changes are indicative of microbial preferences for particular growth conditions, results from this and future BONCAT-FACS studies could inform the development of cultivation media to specifically enrich uncultured microbes. Most importantly, BONCAT-FACS is capable of providing information on the physiology of uncultured organisms at as close to in situ conditions as experimentally possible. 

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5. Differential impact of two major polychaete guilds on microbial communities in marine sediments: a microcosm study

   https://doi.org/10.3389/fmars.2023.1119331  

   Deng, Longhui; Fiskal, Annika; Bölsterli, Damian; Meier, Dimitri; Meile, Christof; Lever, Mark Alexander (June 2023, Frontiers in Marine Science)

   Even though sediment macrofauna are widespread in the global seafloor, the influence of these fauna on microbial communities that drive sediment biogeochemical cycles remains poorly understood. According to recent field investigations, macrofaunal activities control bacterial and archaeal community structure in surface sediments, but the inferred mechanisms have not been experimentally verified. Here we use laboratory microcosms to investigate how activities of two major polychaete guilds, the lugworms, represented byAbarenicola pacifica, and the clamworms, represented byNereis vexillosa, influence microbial communities in coastal sediments.A. pacificatreatments show >tenfold increases in microbial cell-specific consumption rates of oxygen and nitrate, largely due to the strong ventilation activity ofA. pacifica. While ventilation resulted in clearly elevated percentages of nitrifying archaea (Nitrosopumilusspp.) in surface sediments, it only minorly affected bacterial community composition. By comparison, reworking – mainly by deposit-feeding ofA. pacifica– had a more pronounced impact on microorganismal communities, significantly driving down abundances of Bacteria and Archaea. Within the Bacteria, lineages that have been linked to the degradation of microalgal biomass (e.g., Flavobacteriaceae and Rhodobacteraceae), were especially affected, consistent with the previously reported selective feeding ofA. pacificaon microalgal detritus. In contrast,N. vexillosa, which is not a deposit feeder, did not significantly influence microbial abundances or microbial community structure. This species also only had a relatively minor impact on rates of oxygen and nitrogen cycling, presumably because porewater exchanges during burrow ventilation by this species were mainly restricted to sediments immediately surrounding the burrows. Collectively our analyses demonstrate that macrofauna with distinct bioturbation modes differ greatly in their impacts on microbial community structure and microbial metabolism in marine sediments. 

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