Scaling approach to microbial interactions in soil across three bioenergy cropping systems

Microbial communities are initiators, controllers, and mediators of biogeochemical processes, and nutrient and carbon cycling within terrestrial environments. Soil health is also maintained by microbial communities, including water retention, organic matter build-up, and aggregation of soil particles. All of these factors combined, create an enormous impact on terrestrial ecosystems, disproportionate to the microbial cell size, influencing everything from plant productivity and diversity, soil habitat maintenance, and the balance between carbon lost to respiration and carbon maintained within soil as organic matter. Inclusion of microbial communities into management decisions is necessary to fully improve sustainability efforts and productivity. This research investigates the interaction of the aboveground management’s impact on microbial community diversity, function, and resiliency. Specifically, the impact of cropping system and nitrogen application on the soil fungal and bacterial community were explored. In addition, local interactions between plants and fungal communities are examined to determine how trait-based approaches can be applied to microbial ecology. Soil itself is examined as a determinant of microbial community diversity, and is demonstrated to have a strong impact on both fungal and bacterial community structure. In compliment, a novel technique utilizing fluorescently labeled cellulose nanocrystals allows us to address ecosystem scale questions regarding cellulose degradation and utilization within a reductionist and tractable approach

Soil depth and grassland origin cooperatively shape microbial community co‐occurrence and function

Many soils are deep, yet soil below 20 cm remains largely unexplored. Exotic plants can have shallower roots than native species, so their impact on microorganisms is anticipated to change with depth. Using environmental DNA and extracellular enzymatic activities, we studied fungal and bacterial community composition, diversity, function, and co-occurrence networks between native and exotic grasslands at soil depths up to 1 m. We hypothesized (1) the composition and network structure of both fungal and bacterial communities will change with increasing depth, and diversity and enzymatic function will decrease; (2) microbial enzymatic function and network connectedness will be lower in exotic grasslands; and (3) irrigation will alter microbial networks, increasing the overall connectedness. Microbial diversity decreased with depth, and community composition was distinctly different between shallow and deeper soil depths with higher numbers of unknown taxa in lower soil depths. Fungal communities differed between native and exotic plant communities. Microbial community networks were strongly shaped by biotic and abiotic factors concurrently and were the only microbial measurement affected by irrigation. In general, fungal communities were more connected in native plant communities than exotic, especially below 10 cm. Fungal networks were also more connected at lower soil depths albeit with fewer nodes. Bacterial communities demonstrated higher complexity, and greater connectedness and nodes, at lower soil depths for native plant communities. Exotic plant communities’ bacterial network connectedness altered at lower soil depths dependent on irrigation treatments. Microbial extracellular enzyme activity for carbon cycling enzymes significantly declined with soil depth, but enzymes associated with nitrogen and phosphorus cycling continued to have similar activities up to 1 m deep. Our results indicate that native and exotic grasslands have significantly different fungal communities in depths up to 1 m and that both fungal and bacterial networks are strongly shaped jointly by plant communities and abiotic factors. Soil depth is independently a major determinant of both fungal and bacterial community structures, functions, and co-occurrence networks and demonstrates further the importance of including soil itself when investigating plant–microbe interactions

Microbial community structure and functions differ between native and novel (exotic-dominated) grassland ecosystems in an 8-year experiment

A Grasslands dominated by non-native (exotic) spe- cies have replaced purely native-dominated areas in many parts of the world forming ‘novel’ ecosystems. Altered precipitation patterns are predicted to exacerbate this trend. It is still poorly understood how soil microbial communities and their functions differ between high diversity native- and low diversity exotic-dominated sites and how altered precipitation will impact this difference. Methods We sampled 64 experimental grassland plots in central Texas with plant species mixtures of either all native or all exotic species; half with summer irrigation. We tested how native vs. exotic plant species mixtures and summer irrigation affected bacterial and fungal community composition and structure, the influence of niche vs. neutral processes for microbial phylotype co- occurrence (C-score analysis), and rates of phosphorus and nitrogen mineralization across an 8-year experiment. Results Native and exotic-dominated plots had sig- nificantly different fungal community composition and structure, but not diversity, throughout the length of the study, while changes in bacterial communities were limited to certain wet and cool years. Nitrogen and phosphorus mineralization rates were higher un- der native plant mixtures and correlated with the abundance of particular fungal species. Microbial communities were more structured in exotic than native grassland plots, especially for the fungal community. Conclusions The results indicate that conversion of native to exotic C4 dominated grasslands will more strongly impact fungal than bacterial community structure. Further- more, these impacts can alter ecosystem functioning be- lowground via changes in nitrogen and phosphorus cycling

Scaling approach to microbial interactions in soil across three bioenergy cropping systems

Microbial communities are initiators, controllers, and mediators of biogeochemical processes, and nutrient and carbon cycling within terrestrial environments. Soil health is also maintained by microbial communities, including water retention, organic matter build-up, and aggregation of soil particles. All of these factors combined, create an enormous impact on terrestrial ecosystems, disproportionate to the microbial cell size, influencing everything from plant productivity and diversity, soil habitat maintenance, and the balance between carbon lost to respiration and carbon maintained within soil as organic matter. Inclusion of microbial communities into management decisions is necessary to fully improve sustainability efforts and productivity. This research investigates the interaction of the aboveground management’s impact on microbial community diversity, function, and resiliency. Specifically, the impact of cropping system and nitrogen application on the soil fungal and bacterial community were explored. In addition, local interactions between plants and fungal communities are examined to determine how trait-based approaches can be applied to microbial ecology. Soil itself is examined as a determinant of microbial community diversity, and is demonstrated to have a strong impact on both fungal and bacterial community structure. In compliment, a novel technique utilizing fluorescently labeled cellulose nanocrystals allows us to address ecosystem scale questions regarding cellulose degradation and utilization within a reductionist and tractable approach.</p

Microbial community structure and functions differ between native and novel (exotic-dominated) grassland ecosystems in an 8-year experiment

A Grasslands dominated by non-native (exotic) spe- cies have replaced purely native-dominated areas in many parts of the world forming ‘novel’ ecosystems. Altered precipitation patterns are predicted to exacerbate this trend. It is still poorly understood how soil microbial communities and their functions differ between high diversity native- and low diversity exotic-dominated sites and how altered precipitation will impact this difference. Methods We sampled 64 experimental grassland plots in central Texas with plant species mixtures of either all native or all exotic species; half with summer irrigation. We tested how native vs. exotic plant species mixtures and summer irrigation affected bacterial and fungal community composition and structure, the influence of niche vs. neutral processes for microbial phylotype co- occurrence (C-score analysis), and rates of phosphorus and nitrogen mineralization across an 8-year experiment. Results Native and exotic-dominated plots had sig- nificantly different fungal community composition and structure, but not diversity, throughout the length of the study, while changes in bacterial communities were limited to certain wet and cool years. Nitrogen and phosphorus mineralization rates were higher un- der native plant mixtures and correlated with the abundance of particular fungal species. Microbial communities were more structured in exotic than native grassland plots, especially for the fungal community. Conclusions The results indicate that conversion of native to exotic C4 dominated grasslands will more strongly impact fungal than bacterial community structure. Further- more, these impacts can alter ecosystem functioning be- lowground via changes in nitrogen and phosphorus cycling.This article is published as Sielaff, Aleksandra Checinska, Racheal N. Upton, Kirsten S. Hofmockel, Xia Xu, H. Wayne Polley, and Brian J. Wilsey. "Microbial community structure and functions differ between native and novel (exotic-dominated) grassland ecosystems in an 8-year experiment." Plant and Soil 432 (2018): 359-372. doi: 10.1007/s11104-018-3796-1.</p

Soil depth and grassland origin cooperatively shape microbial community co‐occurrence and function

Many soils are deep, yet soil below 20 cm remains largely unexplored. Exotic plants can have shallower roots than native species, so their impact on microorganisms is anticipated to change with depth. Using environmental DNA and extracellular enzymatic activities, we studied fungal and bacterial community composition, diversity, function, and co-occurrence networks between native and exotic grasslands at soil depths up to 1 m. We hypothesized (1) the composition and network structure of both fungal and bacterial communities will change with increasing depth, and diversity and enzymatic function will decrease; (2) microbial enzymatic function and network connectedness will be lower in exotic grasslands; and (3) irrigation will alter microbial networks, increasing the overall connectedness. Microbial diversity decreased with depth, and community composition was distinctly different between shallow and deeper soil depths with higher numbers of unknown taxa in lower soil depths. Fungal communities differed between native and exotic plant communities. Microbial community networks were strongly shaped by biotic and abiotic factors concurrently and were the only microbial measurement affected by irrigation. In general, fungal communities were more connected in native plant communities than exotic, especially below 10 cm. Fungal networks were also more connected at lower soil depths albeit with fewer nodes. Bacterial communities demonstrated higher complexity, and greater connectedness and nodes, at lower soil depths for native plant communities. Exotic plant communities’ bacterial network connectedness altered at lower soil depths dependent on irrigation treatments. Microbial extracellular enzyme activity for carbon cycling enzymes significantly declined with soil depth, but enzymes associated with nitrogen and phosphorus cycling continued to have similar activities up to 1 m deep. Our results indicate that native and exotic grasslands have significantly different fungal communities in depths up to 1 m and that both fungal and bacterial networks are strongly shaped jointly by plant communities and abiotic factors. Soil depth is independently a major determinant of both fungal and bacterial community structures, functions, and co-occurrence networks and demonstrates further the importance of including soil itself when investigating plant–microbe interactions.This article is published as Upton, Racheal N., Aleksandra Checinska Sielaff, Kirsten S. Hofmockel, Xia Xu, H. Wayne Polley, and Brian J. Wilsey. "Soil depth and grassland origin cooperatively shape microbial community co‐occurrence and function." Ecosphere 11, no. 1 (2020). doi: 10.1002/ecs2.2973.</p