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1. Microbial signatures of protected and impacted Northern Caribbean reefs: changes from Cuba to the Florida Keys

   https://doi.org/10.1111/1462-2920.14870  

   Weber, Laura; González‐Díaz, Patricia; Armenteros, Maickel; Ferrer, Víctor_M; Bretos, Fernando; Bartels, Erich; Santoro, Alyson_E; Apprill, Amy (December 2019, Environmental Microbiology)

   Summary There are a few baseline reef‐systems available for understanding the microbiology of healthy coral reefs and their surrounding seawater. Here, we examined the seawater microbial ecology of 25 Northern Caribbean reefs varying in human impact and protection in Cuba and the Florida Keys, USA, by measuring nutrient concentrations, microbial abundances, and respiration rates as well as sequencing bacterial and archaeal amplicons and community functional genes. Overall, seawater microbial composition and biogeochemistry were influenced by reef location and hydrogeography. Seawater from the highly protected ‘crown jewel’ offshore reefs in Jardines de la Reina, Cuba had low concentrations of nutrients and organic carbon, abundantProchlorococcus, and high microbial community alpha diversity. Seawater from the less protected system of Los Canarreos, Cuba had elevated microbial community beta‐diversity whereas waters from the most impacted nearshore reefs in the Florida Keys contained high organic carbon and nitrogen concentrations and potential microbial functions characteristic of microbialized reefs. Each reef system had distinct microbial signatures and within this context, we propose that the protection and offshore nature of Jardines de la Reina may preserve the oligotrophic paradigm and the metabolic dependence of the community on primary production by picocyanobacteria. 

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2. Microbial Cycling of Sulfur and Other Redox‐Sensitive Elements in Porewaters of San Clemente Basin, California, and Cocos Ridge, Costa Rica

   https://doi.org/10.1111/gbi.70013  

   Osorio‐Rodriguez, Daniela; Pavia, Frank J; Utter, Daniel R; Quinan, Matthew; Landry, Kameko; Gomes, Maya; Dalleska, Nathan D; Orphan, Victoria J; Berelson, William M; Adkins, Jess F (February 2025, Geobiology)

   ABSTRACT The microbial recycling of organic matter in marine sediments depends upon electron acceptors that are utilized based on availability and energetic yield. Since sulfate is the most abundant oxidant once oxygen has been depleted, the sulfide produced after sulfate reduction becomes an important electron donor for autotrophic microbes. The ability of sulfide to be re‐oxidized through multiple metabolic pathways and intermediates with variable oxidation states prompts investigation into which species are preferentially utilized and what are the factors that determine the fate of reduced sulfur species. Quantifying these sulfur intermediates in porewaters is a critical first step towards achieving a more complete understanding of the oxidative sulfur cycle, yet this has been accomplished in very few studies, none of which include oligotrophic sedimentary environments in the open ocean. Here we present profiles of porewater sulfur intermediates from sediments underlying oligotrophic regions of the ocean, which encompass about 75% of the ocean's surface and are characterized by low nutrient levels and productivity. Aiming at addressing uncertainties about if and how sulfide produced by the degradation of scarce sedimentary organic matter plays a role in carbon fixation in the sediment, we determine depth profiles of redox‐sensitive metals and sulfate isotope compositions and integrate these datasets with 16S rRNA microbial community composition data and solid‐phase sulfur concentrations. We did not find significant correlations between sulfur species or trace metals and specific sulfur cycling taxa, which suggests that microorganisms in pelagic and oxic sediments may be generalists utilizing flexible metabolisms to oxidize organic matter through different electron acceptors. 

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3. Phylogenomic analysis of novel Diaforarchaea is consistent with sulfite but not sulfate reduction in volcanic environments on early Earth

   https://doi.org/10.1038/s41396-020-0611-9  

   Colman, Daniel R.; Lindsay, Melody R.; Amenabar, Maximiliano J.; Fernandes-Martins, Maria C.; Roden, Eric R.; Boyd, Eric S. (February 2020, The ISME Journal)

   Abstract The origin(s) of dissimilatory sulfate and/or (bi)sulfite reducing organisms (SRO) remains enigmatic despite their importance in global carbon and sulfur cycling since at least 3.4 Ga. Here, we describe novel, deep-branching archaeal SRO populations distantly related to other Diaforarchaea from two moderately acidic thermal springs. Dissimilatory (bi)sulfite reductase homologs, DsrABC, encoded in metagenome assembled genomes (MAGs) from spring sediments comprise one of the earliest evolving Dsr lineages. DsrA homologs were expressed in situ under moderately acidic conditions. MAGs lacked genes encoding proteins that activate sulfate prior to (bi)sulfite reduction. This is consistent with sulfide production in enrichment cultures provided sulfite but not sulfate. We suggest input of volcanic sulfur dioxide to anoxic spring-water yields (bi)sulfite and moderately acidic conditions that favor its stability and bioavailability. The presence of similar volcanic springs at the time SRO are thought to have originated (>3.4 Ga) may have supplied (bi)sulfite that supported ancestral SRO. These observations coincide with the lack of inferred SO42− reduction capacity in nearly all organisms with early-branching DsrAB and which are near universally found in hydrothermal environments. 

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4. Omics-Inferred Partitioning and Expression of Diverse Biogeochemical Functions in a Low-O ₂ Cyanobacterial Mat Community

   https://doi.org/10.1128/mSystems.01042-21  

   Grim, Sharon L.; Voorhies, Alexander A.; Biddanda, Bopaiah A.; Jain, Sunit; Nold, Stephen C.; Green, Russ; Dick, Gregory J. (December 2021, mSystems)

   Bernstein, Hans C. (Ed.)

   ABSTRACT Cyanobacterial mats profoundly influenced Earth’s biological and geochemical evolution and still play important ecological roles in the modern world. However, the biogeochemical functioning of cyanobacterial mats under persistent low-O 2 conditions, which dominated their evolutionary history, is not well understood. To investigate how different metabolic and biogeochemical functions are partitioned among community members, we conducted metagenomics and metatranscriptomics on cyanobacterial mats in the low-O 2 , sulfidic Middle Island sinkhole (MIS) in Lake Huron. Metagenomic assembly and binning yielded 144 draft metagenome assembled genomes, including 61 of medium quality or better, and the dominant cyanobacteria and numerous Proteobacteria involved in sulfur cycling. Strains of a Phormidium autumnale -like cyanobacterium dominated the metagenome and metatranscriptome. Transcripts for the photosynthetic reaction core genes psaA and psbA were abundant in both day and night. Multiple types of psbA genes were expressed from each cyanobacterium, and the dominant psbA transcripts were from an atypical microaerobic type of D1 protein from Phormidium . Further, cyanobacterial transcripts for photosystem I genes were more abundant than those for photosystem II, and two types of Phormidium sulfide quinone reductase were recovered, consistent with anoxygenic photosynthesis via photosystem I in the presence of sulfide. Transcripts indicate active sulfur oxidation and reduction within the cyanobacterial mat, predominately by Gammaproteobacteria and Deltaproteobacteria , respectively. Overall, these genomic and transcriptomic results link specific microbial groups to metabolic processes that underpin primary production and biogeochemical cycling in a low-O 2 cyanobacterial mat and suggest mechanisms for tightly coupled cycling of oxygen and sulfur compounds in the mat ecosystem. IMPORTANCE Cyanobacterial mats are dense communities of microorganisms that contain photosynthetic cyanobacteria along with a host of other bacterial species that play important yet still poorly understood roles in this ecosystem. Although such cyanobacterial mats were critical agents of Earth’s biological and chemical evolution through geological time, little is known about how they function under the low-oxygen conditions that characterized most of their natural history. Here, we performed sequencing of the DNA and RNA of modern cyanobacterial mat communities under low-oxygen and sulfur-rich conditions from the Middle Island sinkhole in Lake Huron. The results reveal the organisms and metabolic pathways that are responsible for both oxygen-producing and non-oxygen-producing photosynthesis as well as interconversions of sulfur that likely shape how much O 2 is produced in such ecosystems. These findings indicate tight metabolic reactions between community members that help to explain the limited the amount of O 2 produced in cyanobacterial mat ecosystems. 

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5. Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom

   https://doi.org/10.1186/s40793-019-0348-0  

   Bhatnagar, Srijak; Cowley, Elise S.; Kopf, Sebastian H.; Pérez Castro, Sherlynette; Kearney, Sean; Dawson, Scott C.; Hanselmann, Kurt; Ruff, S. Emil (December 2020, Environmental Microbiome)

   null (Ed.)

   Abstract Background Lagoons are common along coastlines worldwide and are important for biogeochemical element cycling, coastal biodiversity, coastal erosion protection and blue carbon sequestration. These ecosystems are frequently disturbed by weather, tides, and human activities. Here, we investigated a shallow lagoon in New England. The brackish ecosystem releases hydrogen sulfide particularly upon physical disturbance, causing blooms of anoxygenic sulfur-oxidizing phototrophs. To study the habitat, microbial community structure, assembly and function we carried out in situ experiments investigating the bloom dynamics over time. Results Phototrophic microbial mats and permanently or seasonally stratified water columns commonly contain multiple phototrophic lineages that coexist based on their light, oxygen and nutrient preferences. We describe similar coexistence patterns and ecological niches in estuarine planktonic blooms of phototrophs. The water column showed steep gradients of oxygen, pH, sulfate, sulfide, and salinity. The upper part of the bloom was dominated by aerobic phototrophic Cyanobacteria , the middle and lower parts by anoxygenic purple sulfur bacteria ( Chromatiales ) and green sulfur bacteria ( Chlorobiales ), respectively. We show stable coexistence of phototrophic lineages from five bacterial phyla and present metagenome-assembled genomes (MAGs) of two uncultured Chlorobaculum and Prosthecochloris species. In addition to genes involved in sulfur oxidation and photopigment biosynthesis the MAGs contained complete operons encoding for terminal oxidases. The metagenomes also contained numerous contigs affiliating with Microviridae viruses, potentially affecting Chlorobi . Our data suggest a short sulfur cycle within the bloom in which elemental sulfur produced by sulfide-oxidizing phototrophs is most likely reduced back to sulfide by Desulfuromonas sp . Conclusions The release of sulfide creates a habitat selecting for anoxygenic sulfur-oxidizing phototrophs, which in turn create a niche for sulfur reducers. Strong syntrophism between these guilds apparently drives a short sulfur cycle that may explain the rapid development of the bloom. The fast growth and high biomass yield of Chlorobi -affiliated organisms implies that the studied lineages of green sulfur bacteria can thrive in hypoxic habitats. This oxygen tolerance is corroborated by oxidases found in MAGs of uncultured Chlorobi . The findings improve our understanding of the ecology and ecophysiology of anoxygenic phototrophs and their impact on the coupled biogeochemical cycles of sulfur and carbon. 

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