Vertical and temporal variations of soil bacterial and archaeal communities in wheat-soybean rotation agroecosystem

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.

Stochastic and deterministic processes shape bioenergy crop microbiomes along a vertical soil niche

Sustainable biofuel cropping systems aim to address climate change while meeting energy needs. Understanding how soil and plant-associated microbes respond to these different cropping systems is key to promoting agriculture sustainability and evaluating changes in ecosystem functions. Here, we leverage a long-term biofuel cropping system field experiment to dissect soil and root microbiome changes across a soil-depth gradient in poplar, restored prairie and switchgrass to understand their effects on the microbial communities. High throughput amplicon sequencing of the fungal internal transcribed spacer (ITS) and prokaryotic 16S DNA regions showed a common trend of root and soil microbial community richness decreasing and evenness increasing with depth. Ecological niche (root vs. soil) had the strongest effect on community structure, followed by depth, then crop. Stochastic processes dominated the structuring of fungal communities in deeper soil layers while operational taxonomic units (OTUs) in surface soil layers were more likely to co-occur and to be enriched by plant hosts. Prokaryotic communities were dispersal limited at deeper depths. Microbial networks showed a higher density, connectedness, average degree and module size in deeper soils. We observed a decrease in fungal-fungal links and an increase of bacteria-bacteria links with increasing depth in all crops, particularly in the root microbiome.

Spatial Variation of Microbial Community Structure and Its Driving Environmental Factors in Two Forest Types in Permafrost Region of Greater Xing′an Mountains

Climate warming is accelerating permafrost degradation. Soil microorganisms play key roles in the maintenance of high-latitude permafrost regions and forest ecosystems’ functioning and regulation of biogeochemical cycles. In this study, we used Illumina MiSeq high-throughput sequencing to investigate soil bacterial community composition at a primeval Larix gmelinii forest and a secondary Betula platyphylla forest in a permafrost region of the Greater Xing’an Mountains. The Shannon diversity index tended to decrease and then increase with increasing soil depth, which was significantly higher in the L. gmelinii forest than in the B. platyphylla forest at 40–60 cm. Proteobacteria (19.86–29.68%), Acidobacteria (13.59–31.44%), Chloroflexi (11.04–27.19%), Actinobacteria (7.05–25.57%), Gemmatimonadetes (1.76–9.18%), and Verrucomicrobia (2.03–7.00%) were the predominant phyla of the bacterial community in two forest types. The relative abundance of Proteobacteria showed a decreasing trend in the B. platyphylla forest and an increasing trend in the L. gmelinii forest, whereas that of Chloroflexi increased and then decreased in the B. platyphylla forest and decreased in the L. gmelinii forest with increasing soil depth. The relative abundance of Acidobacteria was significantly higher in the B. platyphylla forest than in the L. gmelinii forest at 0–20 cm depth, whereas that of Actinobacteria was significantly higher in the L. gmelinii forest than in the B. platyphylla forest at 0–20 cm and 40–60 cm depth. Principal coordinate analysis (PCoA) and two-way analysis of variance (ANOVA) indicated that microbial community composition was more significantly influenced by forest type than soil depth. Redundancy analysis (RDA) showed that microbial community structure was strongly affected by soil physicochemical properties such as nitrate nitrogen (NO3−-N), pH, and total organic carbon (TOC). These results offer insights into the potential relationship between soil microbial community and forest conversion in high latitude permafrost ecosystems.