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1. Ecological Dichotomies Arise in Microbial Communities Due to Mixing of Deep Hydrothermal Waters and Atmospheric Gas in a Circumneutral Hot Spring

   https://doi.org/10.1128/AEM.01598-21  

   Fernandes-Martins, Maria C. ; Keller, Lisa M. ; Munro-Ehrlich, Mason ; Zimlich, Kathryn R. ; Mettler, Madelyn K. ; England, Alexis M. ; Clare, Rita ; Surya, Kevin ; Shock, Everett L. ; Colman, Daniel R. ; et al ( November 2021 , Applied and Environmental Microbiology)

   Semrau, Jeremy D. (Ed.)

   ABSTRACT Little is known of how the confluence of subsurface and surface processes influences the assembly and habitability of hydrothermal ecosystems. To address this knowledge gap, the geochemical and microbial composition of a high-temperature, circumneutral hot spring in Yellowstone National Park was examined to identify the sources of solutes and their effect on the ecology of microbial inhabitants. Metagenomic analysis showed that populations comprising planktonic and sediment communities are archaeal dominated, are dependent on chemical energy (chemosynthetic), share little overlap in their taxonomic composition, and are differentiated by their inferred use of/tolerance to oxygen and mode of carbon metabolism. The planktonic community is dominated by putative aerobic/aerotolerant autotrophs, while the taxonomic composition of the sediment community is more evenly distributed and comprised of anaerobic heterotrophs. These observations are interpreted to reflect sourcing of the spring by anoxic, organic carbon-limited subsurface hydrothermal fluids and ingassing of atmospheric oxygen that selects for aerobic/aerotolerant organisms that have autotrophic capabilities in the water column. Autotrophy and consumption of oxygen by the planktonic community may influence the assembly of the anaerobic and heterotrophic sediment community. Support for this inference comes from higher estimated rates of genome replication in planktonic populations than sediment populations, indicating faster growth in planktonic populations. Collectively, these observations provide new insight into how mixing of subsurface waters and atmospheric oxygen create dichotomy in the ecology of hot spring communities and suggest that planktonic and sediment communities may have been less differentiated taxonomically and functionally prior to the rise of oxygen at ∼2.4 billion years ago (Gya). IMPORTANCE Understanding the source and availability of energy capable of supporting life in hydrothermal environments is central to predicting the ecology of microbial life on early Earth when volcanic activity was more widespread. Little is known of the substrates supporting microbial life in circumneutral to alkaline springs, despite their relevance to early Earth habitats. Using metagenomic and informatics approaches, water column and sediment habitats in a representative circumneutral hot spring in Yellowstone were shown to be dichotomous, with the former largely hosting aerobic/aerotolerant autotrophs and the latter primarily hosting anaerobic heterotrophs. This dichotomy is attributed to influx of atmospheric oxygen into anoxic deep hydrothermal spring waters. These results indicate that the ecology of microorganisms in circumneutral alkaline springs sourced by deep hydrothermal fluids was different prior to the rise of atmospheric oxygen ∼2.4 Gya, with planktonic and sediment communities likely to be less differentiated than contemporary circumneutral hot springs. 

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2. Habitat complexity, connectivity, and introduced fish drive pond community structure along an urban to rural gradient

   https://doi.org/10.1002/eap.2828  

   Trovillion, Daniel C. ; Sauer, Erin L. ; Shay, Gabrielle ; Crone, Erin R. ; Preston, Daniel L. ( March 2023 , Ecological Applications)

   Urbanization can influence local richness (alpha diversity) and community composition (beta diversity) in numerous ways. For instance, reduced connectivity and land cover change may lead to the loss of native specialist taxa, decreasing alpha diversity. Alternatively, if urbanization facilitates nonnative species introductions and generalist taxa, alpha diversity may remain unchanged or increase, while beta diversity could decline due to the homogenization of community structure. Wetlands and ponds provide critical ecosystem services and support diverse communities, making them important systems in which to understand the consequences of urbanization. To determine how urban development shapes pond community structure, we surveyed 68 ponds around Madison, Wisconsin, USA, which were classified as urban, greenspace, or rural based on surrounding land use. We evaluated how landscape and local pond factors were correlated with the alpha diversity of aquatic plants, macroinvertebrates, and aquatic vertebrates. We also analyzed whether surrounding land use was associated with changes in community composition and the presence of specific taxa. We found a 23% decrease in mean richness (alpha diversity) from rural to urban pond sites and a 15% decrease from rural to greenspace pond sites. Among landscape factors, adjacent developed land, mowed lawn cover, and greater distances to other waterbodies were negatively correlated with observed pond richness. Among pond level factors, habitat complexity was associated with increased richness, while nonnative fishes were associated with decreased richness. Beta diversity was relatively high for all ponds due to turnover in composition between sites. Urban ponds supported more nonnative species, lacked a subset of native species found in rural ponds, and had slightly higher beta diversity than greenspace and rural ponds. Our results suggest that integrating ponds into connected greenspaces, maintaining riparian vegetation, preventing nonnative fish introductions, and promoting habitat complexity may mitigate the negative effects of urbanization on aquatic richness. While ponds are small in size and rarely incorporated into urban conservation planning, the high beta diversity of distinct pond communities emphasizes their importance for supporting urban biodiversity.

    

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3. Seafloor incubation experiments at deep-sea hydrothermal vents reveal distinct biogeographic signatures of autotrophic communities

   https://doi.org/10.1093/femsec/fiae001  

   Fullerton, Heather ; Smith, Lindsey ; Enriquez, Alejandra ; Butterfield, David ; Wheat, C. Geoffrey ; Moyer, Craig L. ( January 2024 , FEMS Microbiology Ecology)

   The discharge of hydrothermal vents on the seafloor provides energy sources for dynamic and productive ecosystems, which are supported by chemosynthetic microbial populations. These populations use the energy gained by oxidizing the reduced chemicals contained within the vent fluids to fix carbon and support multiple trophic levels. Hydrothermal discharge is ephemeral and chemical composition of such fluids varies over space and time, which can result in geographically distinct microbial communities. To investigate the foundational members of the community, microbial growth chambers were placed within the hydrothermal discharge at Axial Seamount (Juan de Fuca Ridge), Magic Mountain Seamount (Explorer Ridge), and Kamaʻehuakanaloa Seamount (Hawai'i hotspot). Campylobacteria were identified within the nascent communities, but different amplicon sequence variants were present at Axial and Kamaʻehuakanaloa Seamounts, indicating that geography in addition to the composition of the vent effluent influences microbial community development. Across these vent locations, dissolved iron concentration was the strongest driver of community structure. These results provide insights into nascent microbial community structure and shed light on the development of diverse lithotrophic communities at hydrothermal vents.

    

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4. Aqueous Geochemical and Microbial Variation Across Discrete Depth Intervals in a Peridotite Aquifer Assessed Using a Packer System in the Samail Ophiolite, Oman

   https://doi.org/10.1029/2021JG006319  

   Nothaft, Daniel B. ; Templeton, Alexis S. ; Boyd, Eric S. ; Matter, Juerg M. ; Stute, Martin ; Paukert Vankeuren, Amelia N. ; The Oman Drilling Project Science Team ( September 2021 , Journal of Geophysical Research: Biogeosciences)

   The potential for molecular hydrogen () generated via serpentinization to fuel subsurface microbial ecosystems independent from photosynthesis has prompted biogeochemical investigations of serpentinization‐influenced fluids. However, investigations typically sample via surface seeps or open‐borehole pumping, which can mix chemically distinct waters from different depths. Depth‐indiscriminate sampling methods could thus hinder understanding of the spatial controls on nutrient availability for microbial life. To resolve distinct groundwaters in a low‐temperature serpentinizing environment, we deployed packers (tools that seal against borehole walls during pumping) in two‐deep, peridotite‐hosted wells in the Samail Ophiolite, Oman. Isolation and pumping of discrete intervals as deep astobelow ground level revealed multiple aquifers that ranged in pH from 8 to 11. Chemical analyses and 16S rRNA gene sequencing of deep, highly reactedgroundwaters bearing up to,methane () andsulfate () revealed an ecosystem dominated by Bacteria affiliated with the class Thermodesulfovibrionia, a group of chemolithoheterotrophs supported byoxidation coupled toreduction. In shallower, oxidizedgroundwaters, aerobic and denitrifying heterotrophs were relatively more abundant. Highandof(up toand, respectively) indicated microbialoxidation, particularly inwaters with evidence of mixing withwaters. This study demonstrates the power of spatially resolving groundwaters to probe their distinct geochemical conditions and chemosynthetic communities. Such information will help improve predictions of where microbial activity in fractured rock ecosystems might occur, including beyond Earth.

    

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5. Seasonal hydrologic and geologic forcing drive hot spring geochemistry and microbial biodiversity

   https://doi.org/10.1111/1462-2920.15617  

   Colman, Daniel R. ; Lindsay, Melody R. ; Harnish, Annette ; Bilbrey, Evan M. ; Amenabar, Maximiliano J. ; Selensky, Matthew J. ; Fecteau, Kristopher M. ; Debes, II, Randall V. ; Stott, Matthew B. ; Shock, Everett L. ; et al ( June 2021 , Environmental Microbiology)

   Hot springs integrate hydrologic and geologic processes that vary over short‐ and long‐term time scales. However, the influence of temporal hydrologic and geologic change on hot spring biodiversity is unknown. Here, we coordinated near‐weekly, cross‐seasonal (~140 days) geochemical and microbial community analyses of three widely studied hot springs with local precipitation data in Yellowstone National Park. One spring (‘HFS’) exhibited statistically significant, coupled microbial and geochemical variation across seasons that was associated with recent precipitation patterns. Two other spring communities, ‘CP’ and ‘DS’, exhibited minimal to no variation across seasons. Variability in the seasonal response of springs is attributed to differences in the timing and extent of aquifer recharge with oxidized near‐surface water from precipitation. This influx of oxidized water is associated with changes in community composition, and in particular, the abundances of aerobic sulfide‐/sulfur‐oxidizers that can acidify waters. During sampling, a new spring formed after a period of heavy precipitation and its successional dynamics were also influenced by surface water recharge. Collectively, these results indicate that changes in short‐term hydrology associated with precipitation can impact hot spring geochemistry and microbial biodiversity. These results point to potential susceptibility of certain hot springs and their biodiversity to sustained, longer‐term hydrologic changes.

    

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