Seasonal, sub-seasonal and diurnal variation of soil bacterial community composition in a temperate deciduous forest

Seasonal effects of long-term warming on ecosystem function and bacterial diversity

Across biomes, soil biodiversity promotes ecosystem functions. However, whether this relationship will be maintained within ecosystems under climate change is uncertain. Here, using two long-term soil warming experiments, we investigated how warming affects the relationship between ecosystem functions and bacterial diversity across seasons, soil horizons, and warming duration. Soils were sampled from these warming experiments located at the Harvard Forest Long-Term Ecological Research (LTER) site, where soils had been heated +5°C above ambient for 13 or 28 years at the time of sampling. We assessed seven measurements representative of different ecosystem functions and nutrient pools. We also surveyed bacterial community diversity. We found that ecosystem function was significantly affected by season, with autumn samples having a higher intercept than summer samples in our model, suggesting a higher overall baseline of ecosystem function in the fall. The effect of warming on bacterial diversity was similarly affected by season, where warming in the summer was associated with decreased bacterial evenness in the organic horizon. Despite the decreased bacterial evenness in the warmed plots, we found that the relationship between ecosystem function and bacterial diversity was unaffected by warming or warming duration. Our findings highlight that season is a consistent driver of ecosystem function as well as a modulator of climate change effects on bacterial community evenness.

Fire-Induced Changes in Soil Properties and Bacterial Communities in Rotational Shifting Cultivation Fields in Northern Thailand

Fire is a common practice in rotational shifting cultivation (RSC), but little is known about the dynamics of bacterial populations and the impact of fire disturbance in northern Thailand. To fill the research gap, this study aims to investigate the dynamics of soil bacterial communities and examine how the soil's physicochemical properties influence the bacterial communities in RSC fields over a period of one year following a fire. Surface soil samples (0-2 cm depth) were collected from sites with 6 (RSC-6Y) and 12 (RSC-12Y) years of fallow in Chiang Mai Province, northern Thailand at six different time points: before burning, 5 min after burning (summer), 3 months after burning (rainy season), 6 months after burning (rainy season), 9 months after burning (winter), and 12 months after burning (summer). The results revealed a reduction in the soil bacterial communities' diversity and an increase in soil nutrient levels immediately after the fire. The fire significantly influenced the abundance of Firmicutes, Proteobacteria, Acidobacteria, and Planctomycetes, but not that of Actinobacteria. At the genus level, Bacillus, Conexibacter, and Chthoniobacter showed increased abundance following the fire. During the rainy season, a recovery in the abundance of the soil bacterial communities was observed, although soil nutrient availability declined. Soil physicochemical properties such as pH, organic matter, organic carbon, electrical conductivity, cation exchange capacity, nitrate-nitrogen, available phosphorus, exchangeable potassium, total nitrogen, bulk density, sand, and silt contents significantly influenced the composition of bacterial communities. Alpha diversity indices indicated a decrease in diversity immediately after burning, followed by an increase from the early rainy season until the summer season, indicating that seasonal variation affected the composition of the soil bacterial communities. After one year of burning, an increase in bacterial richness was observed, while the diversity of the bacterial communities reverted to pre-burning levels.

Light-dark cycles may influence in situ soil bacterial networks and diurnally-sensitive taxa

Soil bacterial taxa have important functional roles in ecosystems (e.g. nutrient cycling, soil formation, plant health). Many factors influence their assembly and regulation, with land cover types (e.g. open woodlands, grasslands), land use types (e.g. nature reserves, urban green space) and plant-soil feedbacks being well-studied factors. However, changes in soil bacterial communities in situ over light-dark cycles have received little attention, despite many plants and some bacteria having endogenous circadian rhythms that could influence soil bacterial communities. We sampled surface soils in situ across 24-h light-dark cycles (at 00:00, 06:00, 12:00, 18:00) at two land cover types (remnant vegetation vs. cleared, grassy areas) and applied 16S rRNA amplicon sequencing to investigate changes in bacterial communities. We show that land cover type strongly affected soil bacterial diversity, with soils under native vegetation expressing 15.4%-16.4% lower alpha diversity but 4.9%-10.6% greater heterogeneity than soils under cleared vegetation. In addition, we report time-dependent and site-specific changes in bacterial network complexity and between 598-922 ASVs showing significant changes in relative abundance across times. Native site node degree (bacterial interactions) at the phylum level was 16.0% higher in the early morning than in the afternoon/evening. Our results demonstrate for the first time that light-dark cycles have subtle yet important effects on soil bacterial communities in situ and that land cover influences these dynamics. We provide a new view of soil microbial ecology and suggest that future studies should consider the time of day when sampling soil bacteria.

Impacts of sample handling and storage conditions on archiving physiologically active soil microbial communities

Soil microbial communities are fundamental to ecosystem processes and plant growth, yet community composition is seasonally and successionally dynamic, which interferes with long-term iterative experimentation of plant-microbe interactions. We explore how soil sample handling (e.g. filtering) and sample storage conditions impact the ability to revive the original, physiologically active, soil microbial community. We obtained soil from agricultural fields in Montana and Oklahoma, USA and samples were sieved to 2 mm or filtered to 45 µm. Sieved and filtered soil samples were archived at -20°C or -80°C for 50 days and revived for 2 or 7 days. We extracted DNA and the more transient RNA pools from control and treatment samples and characterized microbial communities using 16S amplicon sequencing. Filtration and storage treatments significantly altered soil microbial communities, impacting both species richness and community composition. Storing sieved soil at -20°C did not alter species richness and resulted in the least disruption to the microbial community composition in comparison to nonarchived controls as characterized by RNA pools from soils of both sites. Filtration significantly altered composition but not species richness. Archiving sieved soil at -20°C could allow for long-term and repeated experimentation on preserved physiologically active microbial communities.

The gut microbiome mediates adaptation to scarce food in Coleoptera

Beetles are ubiquitous cave invertebrates worldwide that adapted to scarce subterranean resources when they colonized caves. Here, we investigated the potential role of gut microbiota in the adaptation of beetles to caves from different climatic regions of the Carpathians. The beetles' microbiota was host-specific, reflecting phylogenetic and nutritional adaptation. The microbial community structure further resolved conspecific beetles by caves suggesting microbiota-host coevolution and influences by local environmental factors. The detritivore species hosted a variety of bacteria known to decompose and ferment organic matter, suggesting turnover and host cooperative digestion of the sedimentary microbiota and allochthonous-derived nutrients. The cave Carabidae, with strong mandibula, adapted to predation and scavenging of animal and plant remains, had distinct microbiota dominated by symbiotic lineages Spiroplasma or Wolbachia. All beetles had relatively high levels of fermentative Carnobacterium and Vagococcus involved in lipid accumulation and a reduction of metabolic activity, and both features characterize adaptation to caves.

Regional biogeography versus intra-annual dynamics of the root and soil microbiome

BACKGROUND

Root and soil microbial communities constitute the below-ground plant microbiome, are drivers of nutrient cycling, and affect plant productivity. However, our understanding of their spatiotemporal patterns is confounded by exogenous factors that covary spatially, such as changes in host plant species, climate, and edaphic factors. These spatiotemporal patterns likely differ across microbiome domains (bacteria and fungi) and niches (root vs. soil).

RESULTS

To capture spatial patterns at a regional scale, we sampled the below-ground microbiome of switchgrass monocultures of five sites spanning > 3 degrees of latitude within the Great Lakes region. To capture temporal patterns, we sampled the below-ground microbiome across the growing season within a single site. We compared the strength of spatiotemporal factors to nitrogen addition determining the major drivers in our perennial cropping system. All microbial communities were most strongly structured by sampling site, though collection date also had strong effects; in contrast, nitrogen addition had little to no effect on communities. Though all microbial communities were found to have significant spatiotemporal patterns, sampling site and collection date better explained bacterial than fungal community structure, which appeared more defined by stochastic processes. Root communities, especially bacterial, were more temporally structured than soil communities which were more spatially structured, both across and within sampling sites. Finally, we characterized a core set of taxa in the switchgrass microbiome that persists across space and time. These core taxa represented < 6% of total species richness but > 27% of relative abundance, with potential nitrogen fixing bacteria and fungal mutualists dominating the root community and saprotrophs dominating the soil community.

CONCLUSIONS

Our results highlight the dynamic variability of plant microbiome composition and assembly across space and time, even within a single variety of a plant species. Root and soil fungal community compositions appeared spatiotemporally paired, while root and soil bacterial communities showed a temporal lag in compositional similarity suggesting active recruitment of soil bacteria into the root niche throughout the growing season. A better understanding of the drivers of these differential responses to space and time may improve our ability to predict microbial community structure and function under novel conditions.

Transfer of Nitrogen and Phosphorus From Cattle Manure to Soil and Oats Under Simulative Cattle Manure Deposition

Simulated cattle manure deposition was used to estimate nutrient transfer to soil and oats and to investigate changes in microbial community composition and functional groups in oat rhizospheres. Nutrient absorption and return efficiency were calculated as a series of standard calculation formulas, and total nutrient transfer efficiency was nutrient absorption efficiency plus nutrient return efficiency. In total, 74.83% of nitrogen (N) and 59.30% of phosphorus (P) in cattle manure were transferred to soil and oats, with 11.79% of N and 7.89% of P in cattle manure absorbed by oats, and the remainder sequestered in the soil for 80 days after sowing. Cattle manure increased oat root length, surface, and volume under 0.2 mm diameter, and improved relative abundance of the microbiome known to be beneficial. In response to cattle manure, several bacteria known to be beneficial, such as Proteobacteria, Bacteroidota, and Firmicutes at phyla the level and Pseudoxanthomonas, Pseudomonas, and Sphingomonas at the genus level, were positively related to oat biomass and nutrient accumulation. For fungal communities, the relative abundance of Ascomycota is the predominant phylum, which varied in a larger range in the control treatment (81.0–63.3%) than the cattle manure deposition treatment (37.0–42.9%) as plant growing days extend. The relevant abundance of Basidiomycota known as decomposer was higher in cattle manure deposition treatment compared to that in control treatment at 15 days after sowing. More importantly, cattle manure deposition inhibited trophic mode within pathotroph like Alternaria and Fusarium fungal genus and promoted saprotroph and symbiotroph.

Assessment of Biodegradation and Eco-Toxic Properties of Novel Starch and Gelatine Blend Bioplastics

To combat the release of petroleum-derived plastics into the environment the European Commission has adopted the EU plastics strategy, which aims for a complete ban on single-use plastics by 2030. Environmentally friendly and sustainable packaging like bioplastic is being up taken at significant levels by companies and consumers. In this study, the environmental impact of novel gelatine–starch blend bioplastics is investigated. The assessments included ecotoxicology with different species that can be found in marine and soil environments to simulate natural conditions. Microalgae, plant, and nematode species were chosen as these are representative of their habitats and are known for their sensitivity to pollutants. Degradation rates of these novel bioplastics were assessed as well as microbiome analysis of the soil before and after bioplastic degradation. The main findings of this study are that (i) the bioplastic generated can be fully biodegraded in soil environments at moderate conditions (20 °C) leaving no physical traces; (ii) bioplastic did not exhibit significantly adverse effects on any organisms assessed in this study; (iii) microbiome analysis of the soil after biodegradation showed a decrease in alpha diversity and a significant increase of Actinobacteria and Firmicutes phyla, which were dominative in the soil.

Seasonal Changes in Soil Microbial Community and Co-Occurrence Network of Species of the Genus Corylus

Hazelnut is one of the four major nuts in the world and has high nutritional and economic value. This study employed Illumina sequencing of ITS rDNA and 16S rRNA genes to identify the seasonal changes in soil microbial community, the predominant environmental factors driving microbial community composition, and the differences in soil microbial composition among different species of the genus Corylus. We found that the soil microbial community composition of species of Corylus changed significantly with the change in seasons. Corylus heterophylla and Corylus kweichowensis had more ectomycorrhiza in their soil compared to Corylus avellane. The main factor influencing fungal community composition in soil was the available potassium, while that of bacteria was the total phosphorus content. Co-occurrence network analysis revealed that the ratio of positive interaction to negative interaction in soil of C. heterophylla and Ping’ou (C. heterophylla × C. avellane) was higher, while the negative interaction of soil community structure in C. avellane was greater. The bacterial community was more stable than the fungal community according to microbial diversity and co-occurrence network analyses. The findings of this research may facilitate improvements to the production and soil system management in hazel planting processes.

Variation in Microbial Exposure at the Human-Animal Interface and the Implications for Microbiome-Mediated Health Outcome

The human gut microbiome varies between populations, largely reflecting ecological differences. One ecological variable that is rarely considered but may contribute substantially to microbiome variation is the multifaceted nature of human-animal interfaces. We present the hypothesis that different interactions with animals contribute to shaping the human microbiome globally. We utilize a One Health framework to explore how changes in microbial exposure from human-animal interfaces shape the microbiome and, in turn, contribute to differential human health across populations, focusing on commensal and pathogen exposure, changes in colonization resistance and immune system training, and the potential for other functional shifts. Although human-animal interfaces are known to underlie human health and particularly infectious disease disparities, since their impact on the human microbiome remains woefully understudied, we propose foci for future research. We believe it will be crucial to understand this critical aspect of biology and its impacts on human health around the globe.

Changes in microbial communities at different soil depths through the first rainy season following severe wildfire in North China artificial Pinus tabulaeformis forest

Wildfire could result in dramatic changes to soil temperatures and environments, with immediate, short- or long-lasting impacts on soil microbes. However, relatively little research has documented how fire disturbance, soil depth, time variation and their interactions affect soil microbial communities in wet conditions. This study investigated a severe wildfire influenced on bacterial and fungal communities at four soil depths (0-5, 5-10, 10-15 and 15-20 cm) after two quarters (with similar precipitation and exactly during the rainy season). Soil sampling was conducted in a burned site relative to an undisturbed contiguous site in the North China artificial Pinus tabulaeformis forest. Results indicated that fire had significant effects on bacterial and fungal richness, diversity, composition and structure, including most impacts on the surface mineral soil (0-5 cm) within the first period post-fire and minor impacts on the subsoils (5-20 cm) up to the second period. The microbial richness and some dominant taxa in the undisturbed soils changed with time and depth, suggesting spatiotemporal variation in soil microbial communities although the effects of rainfall were weakened. These differences in microbes between burned and undisturbed soils were mainly driven by soil pH, whereas organic matter and available potassium mediated the distribution of microbial communities along depth and time, respectively. In addition, fungal community was more sensitive to fire and time than bacterial community but an opposite result was found in depth. Nevertheless, soil microbes showed some signs of adaptation to fire. This work advocate that non-intervention should be considered in the short term after a fire or low-intensity water replenishment in the case of aridity.

Stochastic Dispersal Rather Than Deterministic Selection Explains the Spatio-Temporal Distribution of Soil Bacteria in a Temperate Grassland

Spatial and temporal processes shaping microbial communities are inseparably linked but rarely studied together. By Illumina 16S rRNA sequencing, we monitored soil bacteria in 360 stations on a 100 square meter plot distributed across six intra-annual samplings in a rarely managed, temperate grassland. Using a multi-tiered approach, we tested the extent to which stochastic or deterministic processes influenced the composition of local communities. A combination of phylogenetic turnover analysis and null modeling demonstrated that either homogenization by unlimited stochastic dispersal or scenarios, in which neither stochastic processes nor deterministic forces dominated, explained local assembly processes. Thus, the majority of all sampled communities (82%) was rather homogeneous with no significant changes in abundance-weighted composition. However, we detected strong and uniform taxonomic shifts within just nine samples in early summer. Thus, community snapshots sampled from single points in time or space do not necessarily reflect a representative community state. The potential for change despite the overall homogeneity was further demonstrated when the focus shifted to the rare biosphere. Rare OTU turnover, rather than nestedness, characterized abundance-independent β-diversity. Accordingly, boosted generalized additive models encompassing spatial, temporal and environmental variables revealed strong and highly diverse effects of space on OTU abundance, even within the same genus. This pure spatial effect increased with decreasing OTU abundance and frequency, whereas soil moisture – the most important environmental variable – had an opposite effect by impacting abundant OTUs more than the rare ones. These results indicate that – despite considerable oscillation in space and time – the abundant and resident OTUs provide a community backbone that supports much higher β-diversity of a dynamic rare biosphere. Our findings reveal complex interactions among space, time, and environmental filters within bacterial communities in a long-established temperate grassland.