More Like this

1. Genome Streamlining, Proteorhodopsin, and Organic Nitrogen Metabolism in Freshwater Nitrifiers

   https://doi.org/10.1128/mbio.02379-21  

   Podowski, Justin C. ; Paver, Sara F. ; Newton, Ryan J. ; Coleman, Maureen L. ( June 2022 , mBio)

   Giovannoni, Stephen J. (Ed.)

   ABSTRACT Microbial nitrification is a critical process governing nitrogen availability in aquatic systems. Freshwater nitrifiers have received little attention, leaving many unanswered questions about their taxonomic distribution, functional potential, and ecological interactions. Here, we reconstructed genomes to infer the metabolism and ecology of free-living picoplanktonic nitrifiers across the Laurentian Great Lakes, a connected series of five of Earth’s largest lakes. Surprisingly, ammonia-oxidizing bacteria (AOB) related to Nitrosospira dominated over ammonia-oxidizing archaea (AOA) at nearly all stations, with distinct ecotypes prevailing in the transparent, oligotrophic upper lakes compared to Lakes Erie and Ontario. Unexpectedly, one ecotype of Nitrosospira encodes proteorhodopsin, which could enhance survival under conditions where ammonia oxidation is inhibited or substrate limited. Nitrite-oxidizing bacteria (NOB) “ Candidatus Nitrotoga” and Nitrospira fluctuated in dominance, with the latter prevailing in deeper, less-productive basins. Genome reconstructions reveal highly reduced genomes and features consistent with genome streamlining, along with diverse adaptations to sunlight and oxidative stress and widespread capacity for organic nitrogen use. Our findings expand the known functional diversity of nitrifiers and establish their ecological genomics in large lake ecosystems. By elucidating links between microbial biodiversity and biogeochemical cycling, our work also informs ecosystem models of the Laurentian Great Lakes, a critical freshwater resource experiencing rapid environmental change. IMPORTANCE Microorganisms play critical roles in Earth’s nitrogen cycle. In lakes, microorganisms called nitrifiers derive energy from reduced nitrogen compounds. In doing so, they transform nitrogen into a form that can ultimately be lost to the atmosphere by a process called denitrification, which helps mitigate nitrogen pollution from fertilizer runoff and sewage. Despite their importance, freshwater nitrifiers are virtually unexplored. To understand their diversity and function, we reconstructed genomes of freshwater nitrifiers across some of Earth’s largest freshwater lakes, the Laurentian Great Lakes. We discovered several new species of nitrifiers specialized for clear low-nutrient waters and distinct species in comparatively turbid Lake Erie. Surprisingly, one species may be able to harness light energy by using a protein called proteorhodopsin, despite the fact that nitrifiers typically live in deep dark water. Our work reveals the unique biodiversity of the Great Lakes and fills key gaps in our knowledge of an important microbial group, the nitrifiers. 

   more » « less
2. Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen-deficient zones with diverse metabolic potential

   https://doi.org/10.1128/mbio.02918-23  

   Zhang, Irene H. ; Borer, Benedict ; Zhao, Rui ; Wilbert, Steven ; Newman, Dianne K. ; Babbin, Andrew R. ( March 2024 , mBio)

   Giovannoni, Stephen J. (Ed.)

   Archaea from the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have diverse metabolic capabilities and participate in multiple biogeochemical cycles. While metagenomics and enrichments have revealed that many DPANN are characterized by ultrasmall genomes, few biosynthetic genes, and episymbiotic lifestyles, much remains unknown about their biology. We report 33 new DPANN metagenome-assembled genomes originating from the three global marine oxygen-deficient zones (ODZs), the first from these regions. We survey DPANN abundance and distribution within the ODZ water column, investigate their biosynthetic capabilities, and report potential roles in the cycling of organic carbon, methane, and nitrogen. We test the hypothesis that nitrous oxide reductases found within several ODZ DPANN genomes may enable ultrasmall episymbionts to serve as nitrous oxide consumers when attached to a host nitrous oxide producer. Our results indicate DPANN archaea as ubiquitous residents within the anoxic core of ODZs with the potential to produce or consume key compounds.

    

   more » « less
3. Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits

   https://doi.org/10.1186/s40168-022-01424-7  

   Zhou, Zhichao ; St. John, Emily ; Anantharaman, Karthik ; Reysenbach, Anna-Louise ( December 2022 , Microbiome)

   When deep-sea hydrothermal fluids mix with cold oxygenated fluids, minerals precipitate out of solution and form hydrothermal deposits. These actively venting deep-sea hydrothermal deposits support a rich diversity of thermophilic microorganisms which are involved in a range of carbon, sulfur, nitrogen, and hydrogen metabolisms. Global patterns of thermophilic microbial diversity in deep-sea hydrothermal ecosystems have illustrated the strong connectivity between geological processes and microbial colonization, but little is known about the genomic diversity and physiological potential of these novel taxa. Here we explore this genomic diversity in 42 metagenomes from four deep-sea hydrothermal vent fields and a deep-sea volcano collected from 2004 to 2018 and document their potential implications in biogeochemical cycles.

   Our dataset represents 3635 metagenome-assembled genomes encompassing 511 novel and recently identified genera from deep-sea hydrothermal settings. Some of the novel bacterial (107) and archaeal genera (30) that were recently reported from the deep-sea Brothers volcano were also detected at the deep-sea hydrothermal vent fields, while 99 bacterial and 54 archaeal genera were endemic to the deep-sea Brothers volcano deposits. We report some of the first examples of medium- (≥ 50% complete, ≤ 10% contaminated) to high-quality (> 90% complete, < 5% contaminated) MAGs from phyla and families never previously identified, or poorly sampled, from deep-sea hydrothermal environments. We greatly expand the novel diversity of Thermoproteia, Patescibacteria (Candidate Phyla Radiation, CPR), and Chloroflexota found at deep-sea hydrothermal vents and identify a small sampling of two potentially novel phyla, designated JALSQH01 and JALWCF01. Metabolic pathway analysis of metagenomes provides insights into the prevalent carbon, nitrogen, sulfur, and hydrogen metabolic processes across all sites and illustrates sulfur and nitrogen metabolic “handoffs” in community interactions. We confirm that Campylobacteria and Gammaproteobacteria occupy similar ecological guilds but their prevalence in a particular site is driven by shifts in the geochemical environment.

   Our study of globally distributed hydrothermal vent deposits provides a significant expansion of microbial genomic diversity associated with hydrothermal vent deposits and highlights the metabolic adaptation of taxonomic guilds. Collectively, our results illustrate the importance of comparative biodiversity studies in establishing patterns of shared phylogenetic diversity and physiological ecology, while providing many targets for enrichment and cultivation of novel and endemic taxa.

    

   more » « less
4. Genome‐resolved viral ecology in a marine oxygen minimum zone

   https://doi.org/10.1111/1462-2920.15313  

   Vik, Dean ; Gazitúa, Maria Consuelo ; Sun, Christine L. ; Zayed, Ahmed A. ; Aldunate, Montserrat ; Mulholland, Margaret R. ; Ulloa, Osvaldo ; Sullivan, Matthew B. ( November 2020 , Environmental Microbiology)

   Oxygen minimum zones (OMZs) are critical to marine nitrogen cycling and global climate change. While OMZ microbial communities are relatively well‐studied, little is known about their viruses. Here, we assess the viral community ecology of 22 deeply sequenced viral metagenomes along a gradient of oxygenated to anoxic waters (<0.02 μmol/l O₂) in the Eastern Tropical South Pacific (ETSP) OMZ. We identified 46 127 viral populations (≥5 kb), which augments the known viruses from ETSP by 10‐fold. Viral communities clustered into six groups that correspond to oceanographic features. Oxygen concentration was the predominant environmental feature driving viral community structure. Alpha and beta diversity of viral communities in the anoxic zone were lower than in surface waters, which parallels the low microbial diversity seen in other studies. ETSP viruses were largely endemic, with the majority of shared viruses (87%) also present in other OMZ samples. We detected 543 putative viral‐encoded auxiliary metabolic genes (AMGs), of which some have a distribution that reflects physico‐chemical characteristics across depth. Together these findings provide an ecological baseline for viral community structure, drivers and population variability in OMZs that will help future studies assess the role of viruses in these climate‐critical environments.

    

   more » « less
5. Sulfate reduction and methanogenesis in the hypersaline deep waters and sediments of a perennially ice‐covered lake

   https://doi.org/10.1002/lno.11723  

   Saxton, Matthew A. ; Samarkin, Vladimir A. ; Madigan, Michael T. ; Bowles, Marshall W. ; Sattley, William Matthew ; Schutte, Charles A. ; Joye, Samantha B. ( April 2021 , Limnology and Oceanography)

   Documenting anaerobic microbial metabolisms in hypersaline perennially ice‐covered lakes in Antarctica further refines the environmental limits to life and may reveal rare biogeochemical mechanisms and/or novel microbial catalysts of elemental cycling. We assessed rates of sulfate reduction, methanogenesis, and anaerobic oxidation of methane using radiotracers and generated 16S rRNA gene libraries from the microbial communities inhabiting the deep calcium‐chloride‐rich brine and sediments of Lake Vanda, McMurdo Dry Valleys, Antarctica. Sulfate reduction rates were observed in surface sediments but not in the brine overlying the sediments. Methane formation through the methylotrophic, acetoclastic, and hydrogenotrophic pathways was quantified using¹⁴C‐labeled methylamine, acetate, and CO₂, respectively, and methanogenesis was detected in both the brine and the sediments. Hydrogenotrophic methanogenesis rates were the highest of all substrates tested in the sediments, while methylotrophic methanogenesis was highest in the brines. Anaerobic oxidation of methane was below the limit of detection in both the brines and sediments. The major taxa ofBacteriaandArchaeadetected were most similar to organisms previously observed in hypersaline environments and included examples related to known sulfate‐reducing bacteria other thanDeltaproteobacteria(surprisingly, sulfate‐reducingDeltaproteobacteriawere not observed in this study), and both methanogenic and methanotrophicArchaea. These data indicate an active microbial community in the anoxic brine of Lake Vanda that while similar in terms of community structure and metabolism to other brine habitats, is uniquely evolved to survive in this extreme environment.

    

   more » « less