McDaniel, M. D. | Search bioRxiv

bioRxiv2026

Could microbes be the architects of improved soil structure under Miscanthus x giganteus?

The perennial grass Miscanthus x giganteus (miscanthus) offers a sustainable alternative to traditional biomass feedstocks while improving key soil health parameters, including aggregation. Aggregate stability results from dynamic soil-plant-microbe interactions, yet the relative importance of each factor remains an active research question. Building on previous observations that miscanthus alters soil structure to improve water-holding capacity and aggregate stability, we characterized the communities of soil bacteria and arbuscular mycorrhizal fungi (AMF) across three sites in Iowa, USA, comparing miscanthus to annual maize (Zea mays L.) and non-cropped perennial turfgrass (Poa spp.). We examined whether microbiomes co-varied with soil aggregation and, if so, whether plant cover identity or life history categorization better explained the observed patterns. Bacterial and AMF communities varied across sites and plant types, with signals that life history and plant cover identity both mattered. Aggregate stability aligned with a perennial-annual divergence in microbial beta diversity, while finer-scale differences in community composition and network structure were plant-specific. Soils under perennial plants were enriched in microbial groups positively correlated with aggregate stability; we identified 61 bacterial and 8 AMF "architect" taxa for future study. Within- and cross-kingdom co-occurrence network analysis revealed greater complexity under perennial plants: 1.9-fold more network links in miscanthus bacteria-bacteria networks than in maize, and 1.7-fold more in turfgrass AMF-AMF networks. Miscanthus fundamentally shapes microbial interactions, particularly among bacteria, relating to improved soil physical structure. Understanding these soil-plant-microbe feedbacks advances the development of biomass feedstocks with a portfolio of soil health benefits for next-generation biofuels and bioproducts. IMPORTANCEPerennial bioenergy crops can provide the raw material for biofuels and bioproducts while simultaneously improving soil health. Miscanthus x giganteus (miscanthus) efficiently stabilizes soil aggregates, potentially leading to higher water retention and erosion resistance. Understanding the microbial contributions to these outcomes is key to building resilient, sustainable bioenergy systems. This study highlights the connections between communities of soil microbes--bacteria and arbuscular mycorrhizal fungi--across three sites and three plant covers, including miscanthus, maize, and turfgrass. We identify a guild of potential "microbial architects" linked to soil aggregation and show more interconnected microbial networks under the perennial plant covers compared to annual maize. These insights shed light on the interactions between soil biological communities and soil physical and chemical properties. More broadly, the results may inform efforts to harness plant-associated microbiomes for sustainable biomass production.

microbiology↗

bioRxiv2020

Disproportionate CH4 sink strength from an endemic, sub-alpine Australian soil microbial community

Soil-to-atmosphere methane (CH4) fluxes are dependent on opposing microbial processes of production and consumption. Here we use a soil-vegetation gradient in an Australian sub-alpine ecosystem to examine links between composition of soil microbial communities, and the fluxes of greenhouse gases they regulate. For each soil-vegetation type (forest, grassland, and bog), we measured carbon dioxide (CO2) and CH4 fluxes and their production/consumption at 5-cm intervals to a depth of 30 cm. All soils were sources of CO2, ranging from 49-93 mg CO2 m-2 h-1. Forest soils were strong net sinks for CH4 at rates up to -413 {micro}g CH4 m-2 h-1. Grassland soils varied with some soils acting as sources and some as sinks, but overall averaged -97 {micro}g CH4 m-2 h-1. Bog soils were net sources of CH4 (+340 {micro}g CH4 m-2 h-1). Methanotrophs were dominated by USC in forest and grassland soils, and Candidatus Methylomirabilis sp. in the bog soils. Methylocystis were also detected at relatively low abundance. The potential disproportionately large contribution of these ecosystems to global CH4 oxidation, and poorly understood microbial community regulating it, highlight our dependence on soil ecosystem services in remote locations can be driven by a unique population of soil microbes. Originality-Significance Statement(Identify the key aspects of originality and significance that place the work within the top 10% of current research in environmental microbiology) Novel methanotrophic bacteria have been discovered in recent years, but few studies have examined the total known diversity of methanotrophs together with the net flux of CH4 from soils. We used an ecosystem with a vegetation-soil gradient in the sub-alpine regions of Australia (with extremely strong consumption of atmospheric CH4) to examine microbial and abiotic drivers of CH4 fluxes across this gradient. Recently characterized methanotrophs, either USC in forest and grassland soils, or oxygenic Candidatus Methylomirabilis sp. in the bog soil were dominant. Methanotrophs belonging to the families Methylococcaceae and Methylocystaceae represented only a small minority of the methanotrophs in this ecosystem.

microbiology↗