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1. Taxonomic and functional restoration of tallgrass prairie soil microbial communities in comparison to remnant and agricultural soils

   https://doi.org/10.1093/femsec/fiad120  

   Mason, Cayla_N; Shahar, Shayla; Beals, Kendall_K; Kelley, Scott_T; Lipson, David_A; Swingley, Wesley_D; Barber, Nicholas_A (October 2023, FEMS Microbiology Ecology)

   Abstract Restoring ecosystems requires the re-establishment of diverse soil microbial communities that drive critical ecosystem functions. In grasslands, restoration and management require the application of disturbances like fire and grazing. Disturbances can shape microbial taxonomic composition and potentially functional composition as well. We characterized taxonomic and functional gene composition of soil communities using whole genome shotgun metagenomic sequencing to determine how restored soil communities differed from pre-restoration agricultural soils and original remnant soils, how management affects soil microbes, and whether restoration and management affect the number of microbial genes associated with carbohydrate degradation. We found distinct differences in both taxonomic and functional diversity and composition among restored, remnant, and agricultural soils. Remnant soils had low taxonomic and functional richness and diversity, as well as distinct composition, indicating that restoration of agricultural soils does not re-create soil microbial communities that match remnants. Prescribed fire management increased functional diversity, which also was higher in more recently planted restorations. Finally, restored and post-fire soils included high abundances of genes encoding cellulose-degrading enzymes, so restorations and their ongoing management can potentially support functions important in carbon cycling. 

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2. Landscape characteristics shape surface soil microbiomes in the Chihuahuan Desert

   https://doi.org/10.3389/fmicb.2023.1135800  

   Hansen, Frederick A.; James, Darren K.; Anderson, John P.; Meredith, Christy S.; Dominguez, Andrew J.; Pombubpa, Nuttapon; Stajich, Jason E.; Romero-Olivares, Adriana L.; Salley, Shawn W.; Pietrasiak, Nicole (June 2023, Frontiers in Microbiology)

   Introduction Soil microbial communities, including biological soil crust microbiomes, play key roles in water, carbon and nitrogen cycling, biological weathering, and other nutrient releasing processes of desert ecosystems. However, our knowledge of microbial distribution patterns and ecological drivers is still poor, especially so for the Chihuahuan Desert. Methods This project investigated the effects of trampling disturbance on surface soil microbiomes, explored community composition and structure, and related patterns to abiotic and biotic landscape characteristics within the Chihuahuan Desert biome. Composite soil samples were collected in disturbed and undisturbed areas of 15 long-term ecological research plots in the Jornada Basin, New Mexico. Microbial diversity of cross-domain microbial groups (total Bacteria, Cyanobacteria, Archaea, and Fungi) was obtained via DNA amplicon metabarcode sequencing. Sequence data were related to landscape characteristics including vegetation type, landforms, ecological site and state as well as soil properties including gravel content, soil texture, pH, and electrical conductivity. Results Filamentous Cyanobacteria dominated the photoautotrophic community while Proteobacteria and Actinobacteria dominated among the heterotrophic bacteria. Thaumarchaeota were the most abundant Archaea and drought adapted taxa in Dothideomycetes and Agaricomycetes were most abundant fungi in the soil surface microbiomes. Apart from richness within Archaea ( p  = 0.0124), disturbed samples did not differ from undisturbed samples with respect to alpha diversity and community composition ( p  ≥ 0.05), possibly due to a lack of frequent or impactful disturbance. Vegetation type and landform showed differences in richness of Bacteria, Archaea, and Cyanobacteria but not in Fungi. Richness lacked strong relationships with soil variables. Landscape features including parent material, vegetation type, landform type, and ecological sites and states, exhibited stronger influence on relative abundances and microbial community composition than on alpha diversity, especially for Cyanobacteria and Fungi. Soil texture, moisture, pH, electrical conductivity, lichen cover, and perennial plant biomass correlated strongly with microbial community gradients detected in NMDS ordinations. Discussion Our study provides first comprehensive insights into the relationships between landscape characteristics, associated soil properties, and cross-domain soil microbiomes in the Chihuahuan Desert. Our findings will inform land management and restoration efforts and aid in the understanding of processes such as desertification and state transitioning, which represent urgent ecological and economical challenges in drylands around the world. 

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3. Salinity Impacts the Functional mcrA and dsrA Gene Abundances in Everglades Marshes

   https://doi.org/10.3390/microorganisms11051180  

   Jordan, Deidra S.; Kominoski, John; Servais, Shelby; Mills, DeEtta (May 2023, Microorganisms)

   Coastal wetlands, such as the Everglades, are increasingly being exposed to stressors that have the potential to modify their existing ecological processes because of global climate change. Their soil microbiomes include a population of organisms important for biogeochemical cycling, but continual stresses can disturb the community’s composition, causing functional changes. The Everglades feature wetlands with varied salinity levels, implying that they contain microbial communities with a variety of salt tolerances and microbial functions. Therefore, tracking the effects of stresses on these populations in freshwater and brackish marshes is critical. The study addressed this by utilizing next generation sequencing (NGS) to construct a baseline soil microbial community. The carbon and sulfur cycles were studied by sequencing a microbial functional gene involved in each process, the mcrA and dsrA functional genes, respectively. Saline was introduced over two years to observe the taxonomic alterations that occurred after a long-term disturbance such as seawater intrusion. It was observed that saltwater dosing increased sulfite reduction in freshwater peat soils and decreased methylotrophy in brackish peat soils. These findings add to the understanding of microbiomes by demonstrating how changes in soil qualities impact communities both before and after a disturbance such as saltwater intrusion. 

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4. The Transcriptional Response of Soil Bacteria to Long-Term Warming and Short-Term Seasonal Fluctuations in a Terrestrial Forest

   https://doi.org/10.3389/fmicb.2021.666558  

   Roy Chowdhury, Priyanka; Golas, Stefan M.; Alteio, Lauren V.; Stevens, Joshua T.; Billings, Andrew F.; Blanchard, Jeffrey L.; Melillo, Jerry M.; DeAngelis, Kristen M. (August 2021, Frontiers in Microbiology)

   Terrestrial ecosystems are an important carbon store, and this carbon is vulnerable to microbial degradation with climate warming. After 30 years of experimental warming, carbon stocks in a temperate mixed deciduous forest were observed to be reduced by 30% in the heated plots relative to the controls. In addition, soil respiration was seasonal, as was the warming treatment effect. We therefore hypothesized that long-term warming will have higher expressions of genes related to carbohydrate and lipid metabolism due to increased utilization of recalcitrant carbon pools compared to controls. Because of the seasonal effect of soil respiration and the warming treatment, we further hypothesized that these patterns will be seasonal. We used RNA sequencing to show how the microbial community responds to long-term warming (~30 years) in Harvard Forest, MA. Total RNA was extracted from mineral and organic soil types from two treatment plots (+5°C heated and ambient control), at two time points (June and October) and sequenced using Illumina NextSeq technology. Treatment had a larger effect size on KEGG annotated transcripts than on CAZymes, while soil types more strongly affected CAZymes than KEGG annotated transcripts, though effect sizes overall were small. Although, warming showed a small effect on overall CAZymes expression, several carbohydrate-associated enzymes showed increased expression in heated soils (~68% of all differentially expressed transcripts). Further, exploratory analysis using an unconstrained method showed increased abundances of enzymes related to polysaccharide and lipid metabolism and decomposition in heated soils. Compared to long-term warming, we detected a relatively small effect of seasonal variation on community gene expression. Together, these results indicate that the higher carbohydrate degrading potential of bacteria in heated plots can possibly accelerate a self-reinforcing carbon cycle-temperature feedback in a warming climate. 

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5. Long-term warming in a temperate forest accelerates soil organic matter decomposition despite increased plant-derived inputs

   https://doi.org/10.1007/s10533-024-01165-9  

   San_Román, Atzín X; Srikanthan, Nivetha; Hamid, Andreia A; Muratore, Thomas J; Knorr, Melissa A; Frey, Serita D; Simpson, Myrna J (September 2024, Biogeochemistry)

   Abstract Climate change may alter soil microbial communities and soil organic matter (SOM) composition. Soil carbon (C) cycling takes place over multiple time scales; therefore, long-term studies are essential to better understand the factors influencing C storage and help predict responses to climate change. To investigate this further, soils that were heated by 5 °C above ambient soil temperatures for 18 years were collected from the Barre Woods Soil Warming Study at the Harvard Forest Long-term Ecological Research site. This site consists of large 30 × 30 m plots (control or heated) where entire root systems are exposed to sustained warming conditions. Measurements included soil C and nitrogen concentrations, microbial biomass, and SOM chemistry using gas chromatography–mass spectrometry and solid-state¹³C nuclear magnetic resonance spectroscopy. These complementary techniques provide a holistic overview of all SOM components and a comprehensive understanding of SOM composition at the molecular-level. Our results showed that soil C concentrations were not significantly altered with warming; however, various molecular-level alterations to SOM chemistry were observed. We found evidence for both enhanced SOM decomposition and increased above-ground plant inputs with long-term warming. We also noted shifts in microbial community composition while microbial biomass remained largely unchanged. These findings suggest that prolonged warming induced increased availability of preferred substrates, leading to shifts in the microbial community and SOM biogeochemistry. The observed increase in gram-positive bacteria indicated changes in substrate availability as gram-positive bacteria are often associated with the decomposition of complex organic matter, while gram-negative bacteria preferentially break down simpler organic compounds altering SOM composition over time. Our results also highlight that additional plant inputs do not effectively offset chronic warming-induced SOM decomposition in temperate forests. 

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