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1. High spatial resolution global ocean metagenomes from Bio-GO-SHIP repeat hydrography transects

   https://doi.org/10.1038/s41597-021-00889-9  

   Larkin, Alyse A.; Garcia, Catherine A.; Garcia, Nathan; Brock, Melissa L.; Lee, Jenna A.; Ustick, Lucas J.; Barbero, Leticia; Carter, Brendan R.; Sonnerup, Rolf E.; Talley, Lynne D.; et al (April 2021, Scientific Data)

   Abstract Detailed descriptions of microbial communities have lagged far behind physical and chemical measurements in the marine environment. Here, we present 971 globally distributed surface ocean metagenomes collected at high spatio-temporal resolution. Our low-cost metagenomic sequencing protocol produced 3.65 terabases of data, where the median number of base pairs per sample was 3.41 billion. The median distance between sampling stations was 26 km. The metagenomic libraries described here were collected as a part of a biological initiative for the Global Ocean Ship-based Hydrographic Investigations Program, or “Bio-GO-SHIP.” One of the primary aims of GO-SHIP is to produce high spatial and vertical resolution measurements of key state variables to directly quantify climate change impacts on ocean environments. By similarly collecting marine metagenomes at high spatiotemporal resolution, we expect that this dataset will help answer questions about the link between microbial communities and biogeochemical fluxes in a changing ocean. 

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2. Viral infections likely mediate microbial controls on ecosystem responses to global warming

   https://doi.org/10.1093/femsec/fiad016  

   Wieczynski, Daniel J; Yoshimura, Kristin M; Denison, Elizabeth R; Geisen, Stefan; DeBruyn, Jennifer M; Shaw, A Jonathan; Weston, David J; Pelletier, Dale A; Wilhelm, Steven W; Gibert, Jean P (February 2023, FEMS Microbiology Ecology)

   Abstract Climate change is affecting how energy and matter flow through ecosystems, thereby altering global carbon and nutrient cycles. Microorganisms play a fundamental role in carbon and nutrient cycling and are thus an integral link between ecosystems and climate. Here, we highlight a major black box hindering our ability to anticipate ecosystem climate responses: viral infections within complex microbial food webs. We show how understanding and predicting ecosystem responses to warming could be challenging—if not impossible—without accounting for the direct and indirect effects of viral infections on different microbes (bacteria, archaea, fungi, protists) that together perform diverse ecosystem functions. Importantly, understanding how rising temperatures associated with climate change influence viruses and virus-host dynamics is crucial to this task, yet is severely understudied. In this perspective, we (i) synthesize existing knowledge about virus-microbe-temperature interactions and (ii) identify important gaps to guide future investigations regarding how climate change might alter microbial food web effects on ecosystem functioning. To provide real-world context, we consider how these processes may operate in peatlands—globally significant carbon sinks that are threatened by climate change. We stress that understanding how warming affects biogeochemical cycles in any ecosystem hinges on disentangling complex interactions and temperature responses within microbial food webs. 

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3. Novel metagenome-assembled genomes involved in the nitrogen cycle from a Pacific oxygen minimum zone

   https://doi.org/10.1038/s43705-021-00030-2  

   Sun, Xin; Ward, Bess B. (December 2021, ISME Communications)

   null (Ed.)

   Abstract Oxygen minimum zones (OMZs) are unique marine regions where broad redox gradients stimulate biogeochemical cycles. Despite the important and unique role of OMZ microbes in these cycles, they are less characterized than microbes from the oxic ocean. Here we recovered 39 high- and medium-quality metagenome-assembled genomes (MAGs) from the Eastern Tropical South Pacific OMZ. More than half of these MAGs were not represented at the species level among 2631 MAGs from global marine datasets. OMZ MAGs were dominated by denitrifiers catalyzing nitrogen loss and especially MAGs with partial denitrification metabolism. A novel bacterial genome with nitrate-reducing potential could only be assigned to the phylum level. A Marine-Group II archaeon was found to be a versatile denitrifier, with the potential capability to respire multiple nitrogen compounds including N 2 O. The newly discovered denitrifying MAGs will improve our understanding of microbial adaptation strategies and the evolution of denitrification in the tree of life. 

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4. Feedbacks between phytoplankton and nutrient cycles in a warming ocean

   https://doi.org/10.1038/s41561-024-01454-w  

   Hutchins, David A; Tagliabue, Alessandro (June 2024, Nature Geoscience)

   Climate warming increasingly drives changes in large-scale ocean physics and biogeochemistry, and affects the kinetics of biological reactions. Together these factors govern phytoplankton productivity, thereby shaping the responses of ocean carbon and nutrient cycles to global change. Here we bring together results from experimental, observational and modelling studies to highlight how interactive feedbacks between warming and nutrient limitation can affect the responses of biogeochemically critical marine primary producers. The availability of many bioactive elements in seawater will be altered markedly in the future, thereby shifting resource deficiencies. These modifications to nutrient limitation when compounded by concurrent warming can change phytoplankton optimum growth temperatures and elemental use efficiencies in group-specific and nutrient-specific ways. The biogeochemical impacts of these nutrient and warming interactions reflect a distinction between the thermal reactivity of major cellular structural elements like nitrogen (N) and catalytic micronutrients like iron (Fe). Integrating the mechanistic feedbacks between warming, nutrient availability and primary productivity into Earth system models is necessary to improve confidence in projections of ocean biogeochemical cycle transformations in a changing climate. 

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5. Functional effects of subsidies and stressors on benthic microbial communities along freshwater to marine gradients

   https://doi.org/10.1002/ecy.4427  

   Anderson, Kenneth J; Kominoski, John S; Choi, Chang Jae; Stingl, Ulrich (October 2024, Ecology)

   Abstract Leaf litter in coastal wetlands lays the foundation for carbon storage, and the creation of coastal wetland soils. As climate change alters the biogeochemical conditions and macrophyte composition of coastal wetlands, a better understanding of the interactions between microbial communities, changing chemistry, and leaf litter is required to understand the dynamics of coastal litter breakdown in changing wetlands. Coastal wetlands are dynamic systems with shifting biogeochemical conditions, with both tidal and seasonal redox fluctuations, and marine subsidies to inland habitats. Here, we investigated gene expression associated with various microbial redox pathways to understand how changing conditions are affecting the benthic microbial communities responsible for litter breakdown in coastal wetlands. We performed a reciprocal transplant of leaf litter from four distinct plant species along freshwater‐to‐marine gradients in the Florida Coastal Everglades, tracking changes in environmental and litter biogeochemistry, as well as benthic microbial gene expression associated with varying redox conditions, carbon degradation, and phosphorus acquisition. Early litter breakdown varied primarily by species, with highest breakdown in coastal species, regardless of the site they were at during breakdown, while microbial gene expression showed a strong seasonal relationship between sulfate cycling and salinity, and was not correlated with breakdown rates. The effect of salinity is likely a combination of direct effects, and indirect effects from associated marine subsidies. We found a positive correlation between sulfate uptake and salinity during January with higher freshwater inputs to coastal areas. However, we found a peak of dissimilatory sulfate reduction at intermediate salinity during April when freshwater inputs to coastal sites are lower. The combination of these two results suggests that sulfate acquisition is limiting to microbes when freshwater inputs are high, but that when marine influence increases and sulfate becomes more available, dissimilatory sulfate reduction becomes a key microbial process. As marine influence in coastal wetlands increases with climate change, our study suggests that sulfate dynamics will become increasingly important to microbial communities colonizing decomposing leaf litter. 

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