From pine to pasture: land use history has long-term impacts on soil bacterial community composition and functional potential

"Reflexions on the role, diversity, conservation and management of the genetic microbial resources in Agriculture"

•Soil and its microbial communities play a pivotal role in nutrient cycling, plant growth, and overall ecosystem health.•Over time, the co-evolution of plant-microbe relationships has fostered an interdependence that is central to the microbial loop, significantly contributing to ecosystem functionality.•The ecological and biological dimensions of food production necessitate the adoption of sustainable practices that preserve microbial diversity and promote a holistic management approach to enhance agricultural productivity.•Co-occurrence analysis synthesizes insights across the sections and validates the discussed topics, reinforcing the need for comprehensive scientific understanding to guide effective agricultural practices and policy-making.

Aboveground-belowground linkages across vegetation degradation gradients differ among native eucalypt communities

Native vegetation degradation impacts soil communities and their functions. However, these impacts are often studied by comparing soil biotic attributes across qualitatively defined, discrete degradation levels within a single plant community at a specific location. Direct quantification of the relationships between vegetation and soil attributes across continuous degradation gradients and at larger scales is rare but holds greater potential to reveal robust patterns in aboveground-belowground linkages that may apply across different plant communities. We investigated how native vegetation attributes relate to soil communities and their functions across a degradation gradient within three native temperate eucalypt woodland and forest communities that differed in soil nutrient availabilities. Across remnant patches of native vegetation in the Sydney Basin bioregion, we established plots representing different levels of decline in their vegetation quality (i.e., increased exotics and canopy changes) compared to relevant reference communities. In those plots, we assessed soil community groups (microbes and fauna), carbon (C) and nutrient cycling (litter decomposition, enzyme activity, and phosphate and nitrate accumulation rates), soil pH, texture and vegetation attributes (composition, structure, and function). Our unique study design revealed that the relationships between vegetation degradation and soil biota across the food web (i.e., AM fungi, Fungi:bacteria ratio, Gram-positive bacteria, total nematodes) were highly dependent on the plant community. However, the degradation impacts on soil functions (i.e., total enzyme activity, and phosphate availability) were mostly consistent, suggesting their potential as belowground indicators of ecosystem degradation, with a notable positive association observed in phosphate availability rates. Additionally, the effects of vegetation degradation on soil biota and their functions appeared stronger in the nutrient-poor plant communities, suggesting greater vulnerability of their belowground components. Our findings call for caution when generalizing belowground responses to degradation and for further research on how nutrient availability mediates the impacts of degradation on aboveground-belowground linkages.

Land-use intensification exerts a greater influence on soil microbial communities than seasonal variations in the Taihu Lake region, China

The Taihu Lake region has undergone intensive land-use conversions from natural wetlands (NW) to conventional rice-wheat rotation fields (RW) and further to greenhouse vegetable fields (GH). Nevertheless, the effects of these conversions on soil microbes, particularly in wetland ecosystem, are not well explicit. To explore the impact of land-use intensification on soil microbial communities, monthly soil samples were obtained from replicate plots representing three land-use types (NW, RW, and GH) in subtropical wetlands and then subjected to amplicon sequencing. Land-use intensification had direct effects on bacterial and fungal community composition, with a more pronounced impact on bacteria than on fungi. These changes in bacterial communities were closely correlated with variations in soil environmental variables, such as NO3--N, pH, and electrical conductivity. Land-use intensification led to a decrease in bacterial deterministic processes, with an opposing trend observed in the fungal community. In addition, arable lands (RW and GH), which are affected by anthropogenic activities, exhibited more complex networks. Potential metabolic functional groups in GH had higher absolute abundance. Seasonal variations significantly influenced microbial diversity, composition, and potential metabolic functional groups within each land-use type, particularly in summer, although the magnitude of this impact was much smaller than the impact of land-use intensification. Our findings emphasize the importance of comprehending the ecological consequences of land-use intensification in wetlands for sustainable resource management and biodiversity conservation.

Co-Selection of Bacterial Metal and Antibiotic Resistance in Soil Laboratory Microcosms

Accumulation of heavy metals (HMs) in agricultural soil following the application of superphosphate fertilisers seems to induce resistance of soil bacteria to HMs and appears to co-select for resistance to antibiotics (Ab). This study aimed to investigate the selection of co-resistance of soil bacteria to HMs and Ab in uncontaminated soil incubated for 6 weeks at 25 °C in laboratory microcosms spiked with ranges of concentrations of cadmium (Cd), zinc (Zn) and mercury (Hg). Co-selection of HM and Ab resistance was assessed using plate culture on media with a range of HM and Ab concentrations, and pollution-induced community tolerance (PICT) assays. Bacterial diversity was profiled via terminal restriction fragment length polymorphism (TRFLP) assay and 16S rDNA sequencing of genomic DNA isolated from selected microcosms. Based on sequence data, the microbial communities exposed to HMs were found to differ significantly compared to control microcosms with no added HM across a range of taxonomic levels.

Land use modification causes slow, but predictable, change in soil microbial community composition and functional potential

BACKGROUND

Bacterial communities are critical to ecosystem functioning and sensitive to their surrounding physiochemical environment. However, the impact of land use change on microbial communities remains understudied. We used 16S rRNA gene amplicon sequencing and shotgun metagenomics to assess soil microbial communities' taxonomic and functional responses to land use change. We compared data from long-term grassland, exotic forest and horticulture reference sites to data from sites that transitioned from (i) Grassland to exotic forest or horticulture and from (ii) Exotic forest to grassland.

RESULTS

Community taxonomic and functional profiles of the transitional sites significantly differed from those within reference sites representing both their historic and current land uses (P < 0.001). The bacterial communities in sites that transitioned more recently were compositionally more similar to those representing their historic land uses. In contrast, the composition of communities from sites exposed to older conversion events had shifted towards the compositions at reference sites representing their current land use.

CONCLUSIONS

Our study indicates that microbial communities respond in a somewhat predictable way after a land use conversion event by shifting from communities reflecting their former land use towards those reflecting their current land use. Our findings help us to better understand the legacy effects of land use change on soil microbial communities and implications for their role in soil health and ecosystem functioning. Understanding the responsiveness of microbial communities to environmental disturbances will aid us in incorporating biotic variables into soil health monitoring techniques in the future.

The soil microbiome: An essential, but neglected, component of regenerative agroecosystems

Regenerative agriculture (RA) is gaining traction globally as an approach for meeting growing food demands while avoiding, or even remediating, the detrimental environmental consequences associated with conventional farming. Momentum is building for science to provide evidence for, or against, the putative ecosystem benefits of RA practices relative to conventional farming. In this perspective article, we advance the argument that consideration of the soil microbiome in RA research is crucial for disentangling the varied and complex relationships RA practices have with the biotic and abiotic environment, outline the expected changes in soil microbiomes under RA, and make recommendations for designing research that will answer the outstanding questions on the soil microbiome under RA. Ultimately, deeper insights into the role of microbial communities in RA soils will allow the development of biologically relevant monitoring tools which will support land managers in addressing the key environmental issues associated with agriculture.

Legume Cover Crop Contributions to Ecological Nutrient Management in Upper Midwest Vegetable Systems

Cover cropping, especially with legumes, is a critical approach to ecological soil nutrient management as a means to meet Sustainable Development Goal (SDG) 2, addressing food security issues via sustainable agriculture approaches. However, cover cropping in some of the most intensified food production regions of the northern U.S. is challenged by short growing seasons and harsh winters with variable temperatures and increasingly erratic snowfall. In this study, we explore the potential of winter annual legume cover crops to augment soil organic carbon (C) and nitrogen (N) stocks within a horticultural cropping system under climate conditions that allow only modest cover crop biomass production. We compared hairy vetch, cereal rye, red clover, and a hairy vetch/rye biculture in a randomized complete block design at two sites (North Central and Southwest Research and Outreach Centers in Minnesota) over 2 years. Cover crops were established in fall and terminated in spring prior to sweet corn planting, and soils sampled both at pre-cover crop termination and 2 weeks post-termination. We determined several indicators of C and N dynamics, including microbial biomass C (MBC), permanganate-oxidizable C (POXC), particulate organic matter C and N (POMC and POMN, respectively), extractable soil N (EXTN), and potentially mineralizable N (PMN). Out of all treatments evaluated, vetch production increased soil EXTN the greatest after 2 weeks, contributing two to 11 times more EXTN to soils compared to non-vetch treatments, meeting N requirements for sweet corn in three out of four site-years. Overall, time of sampling, either pre-or post-termination, consistently impacted soil measurements, with p &lt; 0.05 in 20 out of 24 soil parameter × site-year combinations. Study results suggest that cover crops planted in colder northern climates during winter fallow periods can supply valuable N following spring termination, but termination effects on labile C and N pools are mixed. Our findings advance understanding of how cover cropping can support SDG 2 outcomes by assessing cover crop legume systems under biophysical conditions that challenge cover crop integration in agroecosystems.

Historical land use has long-term effects on microbial community assembly processes in forest soils

Land use change has long-term effects on the structure of soil microbial communities, but the specific community assembly processes underlying these effects have not been identified. To investigate effects of historical land use on microbial community assembly, we sampled soils from several currently forested watersheds representing different historical land management regimes (e.g., undisturbed reference, logged, converted to agriculture). We characterized bacterial and fungal communities using amplicon sequencing and used a null model approach to quantify the relative importance of selection, dispersal, and drift processes on bacterial and fungal community assembly. We found that bacterial communities were structured by both selection and neutral (i.e., dispersal and drift) processes, while fungal communities were structured primarily by neutral processes. For both bacterial and fungal communities, selection was more important in historically disturbed soils compared with adjacent undisturbed sites, while dispersal processes were more important in undisturbed soils. Variation partitioning identified the drivers of selection to be changes in vegetation communities and soil properties (i.e., soil N availability) that occur following forest disturbance. Overall, this study casts new light on the effects of historical land use on soil microbial communities by identifying specific environmental factors that drive changes in community assembly.

Short-Term Effect in Soil Microbial Community of Two Strategies of Recovering Degraded Area in Brazilian Savanna: A Pilot Case Study

The Brazilian Cerrado is a highland tropical savanna considered a biodiversity hotspot with many endemic species of plants and animals. Over the years, most of the native areas of this biome became arable areas, and with inadequate management, some are nowadays at varying levels of degradation stage. Crop-livestock integrated systems (CLIS) are one option for the recovery of areas in degradation, improving the physicochemical and biological characteristics of the soil while increasing income and mitigating risks due to product diversification. Little is known about the effect of CLIS on the soil microbial community. Therefore, we perform this pilot case study to support further research on recovering degraded areas. The bacterial and fungal soil communities in the area with CLIS were compared to an area under moderate recovery (low-input recovering - LI) and native savanna (NS) area. Bacterial and fungal communities were investigated by 16S and ITS rRNA gene sequencing (deep rRNA sequencing). Ktedonobacteraceae and AD3 families were found predominantly in LI, confirming the relationship of the members of the Chloroflexi phylum in challenging environmental conditions, which can be evidenced in LI. The CLIS soil presented 63 exclusive bacterial families that were not found in LI or NS and presented a higher bacterial richness, which can be related to good land management. The NS area shared 21 and 6 families with CLIS and LI, respectively, suggesting that the intervention method used in the analyzed period brings microbial diversity closer to the conditions of the native area, demonstrating a trend of approximation between NS and CLIS even in the short term. The most abundant fungal phylum in NS treatment was Basidiomycota and Mucoromycota, whereas Ascomycota predominated in CLIS and LI. The fungal community needs more time to recover and to approximate from the native area than the bacterial community. However, according to the analysis of bacteria, the CLIS area behaved differently from the LI area, showing that this treatment induces a faster response to the increase in species richness, tending to more accelerated recovery. Results obtained herein encourage CLIS as a sustainable alternative for recovery and production in degraded areas.