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1. The Genomic Capabilities of Microbial Communities Track Seasonal Variation in Environmental Conditions of Arctic Lagoons

   https://doi.org/10.3389/fmicb.2021.601901  

   Baker, Kristina D. ; Kellogg, Colleen T. ; McClelland, James W. ; Dunton, Kenneth H. ; Crump, Byron C. ( February 2021 , Frontiers in Microbiology)

   null (Ed.)

   In contrast to temperate systems, Arctic lagoons that span the Alaska Beaufort Sea coast face extreme seasonality. Nine months of ice cover up to ∼1.7 m thick is followed by a spring thaw that introduces an enormous pulse of freshwater, nutrients, and organic matter into these lagoons over a relatively brief 2–3 week period. Prokaryotic communities link these subsidies to lagoon food webs through nutrient uptake, heterotrophic production, and other biogeochemical processes, but little is known about how the genomic capabilities of these communities respond to seasonal variability. Replicate water samples from two lagoons and one coastal site near Kaktovik, AK were collected in April (full ice cover), June (ice break up), and August (open water) to represent winter, spring, and summer, respectively. Samples were size fractionated to distinguish free-living and particle-attached microbial communities. Multivariate analysis of metagenomes indicated that seasonal variability in gene abundances was greater than variability between size fractions and sites, and that June differed significantly from the other months. Spring (June) gene abundances reflected the high input of watershed-sourced nutrients and organic matter via spring thaw, featuring indicator genes for denitrification possibly linked to greater organic carbon availability, and genes for processing phytoplankton-derived organic matter associated with spring blooms. Summer featured fewer indicator genes, but had increased abundances of anoxygenic photosynthesis genes, possibly associated with elevated light availability. Winter (April) gene abundances suggested low energy inputs and autotrophic bacterial metabolism, featuring indicator genes for chemoautotrophic carbon fixation, methane metabolism, and nitrification. Winter indicator genes for nitrification belonged to Thaumarchaeota and Nitrosomonadales, suggesting these organisms play an important role in oxidizing ammonium during the under-ice period. This study shows that high latitude estuarine microbial assemblages shift metabolic capabilities as they change phylogenetic composition between these extreme seasons, providing evidence that these communities may be resilient to large hydrological events in a rapidly changing Arctic. 

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2. Imprint of trace dissolved oxygen on prokaryoplankton community structure in an oxygen minimum zone

   https://doi.org/doi:10.3389/fmars.2020.00360  

   Medina Faull, L. ; Mara, Paraskevi ; Taylor, G.T. ; Edgcomb, V.P. ( January 2020 , Frontiers in marine science)

   null (Ed.)

   The Eastern Tropical North Pacific (ETNP) is a large, persistent, and intensifying oxygen minimum zone (OMZ) that accounts for almost half of the total area of global OMZs. Within the OMZ core (350–700 m depth), dissolved oxygen is typically near or below the analytical detection limit of modern sensors (10 nM). Steep oxygen gradients above and below the OMZ core lead to vertical structuring of microbial communities that also vary between particle-associated (PA) and free-living (FL) size fractions. Here, we use 16S amplicon sequencing (iTags) to analyze the diversity and distribution of prokaryotic populations between FL and PA size fractions and among the range of ambient redox conditions. The hydrographic conditions at our study area were distinct from those previously reported in the ETNP and other OMZs, such as the ETSP. Trace oxygen concentrations (0.35 mM) were present throughout the OMZ core at our sampling location. Consequently, nitrite accumulations typically reported for OMZ cores were absent as were sequences for anammox bacteria (Brocadiales genus Candidatus Scalindua), which are commonly found across oxic-anoxic boundaries in other systems. However, ammonia-oxidizing bacteria (AOB) and archaea (AOA) distributions and maximal autotrophic carbon assimilation rates (1.4 mM C d􀀀1) coincided with a pronounced ammonium concentration maximum near the top of the OMZ core. In addition, members of the genus Nitrospina, a dominant nitrite-oxidizing bacterial (NOB) clade were present suggesting that both ammonia and nitrite oxidation occur at trace oxygen concentrations. Analysis of similarity test (ANOSIM) and Non-metric Dimensional Scaling (nMDS) revealed that bacterial and archaeal phylogenetic representations were significantly different between size fractions. Based on ANOSIM and iTag profiles, composition of PA assemblages was less influenced by the prevailing depth-dependent biogeochemical regime than the FL fraction. Based on the presence of AOA, NOB and trace oxygen in the OMZ core we suggest that nitrification is an active process in the nitrogen cycle of this region of the ETNP OMZ. 

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3. Winter Limnology: How do Hydrodynamics and Biogeochemistry Shape Ecosystems Under Ice?

   https://doi.org/10.1029/2020JG006237  

   Jansen, Joachim ; MacIntyre, Sally ; Barrett, David C. ; Chin, Yu‐Ping ; Cortés, Alicia ; Forrest, Alexander L. ; Hrycik, Allison R. ; Martin, Rosemary ; McMeans, Bailey C. ; Rautio, Milla ; et al ( June 2021 , Journal of Geophysical Research: Biogeosciences)

   The ice‐cover period in lakes is increasingly recognized for its distinct combination of physical and biological phenomena and ecological relevance. Knowledge gaps exist where research areas of hydrodynamics, biogeochemistry and biology intersect. For example, density‐driven circulation under ice coincides with an expansion of the anoxic zone, but abiotic and biotic controls on oxygen depletion have not been disentangled, and while heterotrophic microorganisms and migrating phytoplankton often thrive at the oxycline, the extent to which physical processes induce fluxes of heat and substrates that support under‐ice food webs is uncertain. Similarly, increased irradiance in spring can promote growth of motile phytoplankton or, if radiatively driven convection occurs, more nutritious diatoms, but links between functional trait selection, trophic transfer to zooplankton and fish, and the prevalence of microbial versus classical food webs in seasonally ice‐covered lakes remain unclear. Under‐ice processes cascade into and from the ice‐free season, and are relevant to annual cycling of energy and carbon through aquatic food webs. Understanding the coupling between state transitions and the reorganization of trophic hierarchies is essential for predicting complex ecosystem responses to climate change. In this interdisciplinary review we describe existing knowledge of physical processes in lakes in winter and the parallel developments in under‐ice biogeochemistry and ecology. We then illustrate interactions between these processes, identify extant knowledge gaps and present (novel) methods to address outstanding questions.

    

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4. The core root microbiome of Spartina alterniflora is predominated by sulfur-oxidizing and sulfate-reducing bacteria in Georgia salt marshes, USA

   https://doi.org/10.1186/s40168-021-01187-7  

   Rolando, Jose L. ; Kolton, Max ; Song, Tianze ; Kostka, Joel E. ( December 2022 , Microbiome)

   Abstract Background Salt marshes are dominated by the smooth cordgrass Spartina alterniflora on the US Atlantic and Gulf of Mexico coastlines. Although soil microorganisms are well known to mediate important biogeochemical cycles in salt marshes, little is known about the role of root microbiomes in supporting the health and productivity of marsh plant hosts. Leveraging in situ gradients in aboveground plant biomass as a natural laboratory, we investigated the relationships between S. alterniflora primary productivity, sediment redox potential, and the physiological ecology of bulk sediment, rhizosphere, and root microbial communities at two Georgia barrier islands over two growing seasons. Results A marked decrease in prokaryotic alpha diversity with high abundance and increased phylogenetic dispersion was found in the S. alterniflora root microbiome. Significantly higher rates of enzymatic organic matter decomposition, as well as the relative abundances of putative sulfur (S)-oxidizing, sulfate-reducing, and nitrifying prokaryotes correlated with plant productivity. Moreover, these functional guilds were overrepresented in the S. alterniflora rhizosphere and root core microbiomes. Core microbiome bacteria from the Candidatus Thiodiazotropha genus, with the metabolic potential to couple S oxidation with C and N fixation, were shown to be highly abundant in the root and rhizosphere of S. alterniflora . Conclusions The S. alterniflora root microbiome is dominated by highly active and competitive species taking advantage of available carbon substrates in the oxidized root zone. Two microbially mediated mechanisms are proposed to stimulate S. alterniflora primary productivity: (i) enhanced microbial activity replenishes nutrients and terminal electron acceptors in higher biomass stands, and (ii) coupling of chemolithotrophic S oxidation with carbon (C) and nitrogen (N) fixation by root- and rhizosphere-associated prokaryotes detoxifies sulfide in the root zone while potentially transferring fixed C and N to the host plant. 

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5. Diverse nitrogen cycling pathways across a marine oxygen gradient indicate nitrogen loss coupled to chemoautotrophic activity

   https://doi.org/10.1111/1462-2920.15187  

   Suter, Elizabeth A. ; Pachiadaki, Maria G. ; Montes, Enrique ; Edgcomb, Virginia P. ; Scranton, Mary I. ; Taylor, Craig D. ; Taylor, Gordon T. ( August 2020 , Environmental Microbiology)

   Genetic markers and geochemical assays of microbial nitrogen cycling processes, including autotrophic and heterotrophic denitrification, anammox, ammonia oxidation, and nitrite oxidation, were examined across the oxycline, suboxic, and anoxic zones of the Cariaco Basin, Venezuela. Ammonia and nitrite oxidation genes were expressed through the entire gradient. Transcripts associated with autotrophic and heterotrophic denitrifiers were mostly confined to the suboxic zone and below but were also present in particles in the oxycline. Anammox genes and transcripts were detected over a narrow depth range near the bottom of the suboxic zone and coincided with secondary NO₂⁻maxima and available NH₄⁺. Dissolved inorganic nitrogen (DIN) amendment incubations and comparisons between our sampling campaigns suggested that denitrifier activity may be closely coupled with NO₃⁻availability. Expression of denitrification genes at depths of high rates of chemoautotrophic carbon fixation and phylogenetic analyses of nitrogen cycling genes and transcripts indicated a diverse array of denitrifiers, including chemoautotrophs capable of using NO₃⁻to oxidize reduced sulfur species. Thus, results suggest that the Cariaco Basin nitrogen cycle is influenced by autotrophic carbon cycling in addition to organic matter oxidation and anammox.

    

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