Microbiomes in agroecosystem: Diversity, function and assembly mechanisms

Abstract

Soils are a main repository of biodiversity harbouring immense diversity of microbial species that plays a central role in fundamental ecological processes and acts as the seed bank for emergence of the plant microbiome in cropland ecosystems. Crop‐associated microbiomes play an important role in shaping plant performance, which includes but not limited to nutrient uptake, disease resistance, and abiotic stress tolerance. Although our understanding of structure and function of soil and plant microbiomes has been rapidly advancing, most of our knowledge comes from ecosystems in natural environment. In this review, we present an overview of the current knowledge of diversity and function of microbial communities along the soil–plant continuum in agroecosystems. To characterize the ecological mechanisms for community assembly of soil and crop microbiomes, we explore how crop host and environmental factors such as plant species and developmental stage, pathogen invasion, and land management shape microbiome structure, microbial co‐occurrence patterns, and crop‐microbiome interactions. Particularly, the relative importance of deterministic and stochastic processes in microbial community assembly is illustrated under different environmental conditions, and potential sources and keystone taxa of the crop microbiome are described. Finally, we highlight a few important questions and perspectives in future crop microbiome research.

Periphytic biofilms function as a double‐edged sword influencing nitrogen cycling in paddy fields

“…Periphytic biofilm is essentially a microbial aggregate (Liu et al, 2019; Liu et al, 2021; Sun, Gao, Sun, et al, 2021), and understanding their diversity, composition, and function (e.g. N accumulation and transformation) is crucial for exploiting biofilms for sustainable rice production (Xiong & Lu, 2022). Every microbe needs N to grow; thus, all periphytic biofilm microbes influence their accumulated N. This study determined that N accumulation by periphytic biofilms is a microbe‐driven process, as verified using 16S/18S high‐throughput sequencing and high‐throughput qPCR gene chips.…”

“…Therefore, the difference in abundant and rare microbes mainly induces the difference in the N accumulation potential of periphytic biofilms across China. In further work, the keystone taxa of these biofilms in N accumulation may be identified by multiomics techniques (Xiong & Lu, 2022). The high diversity of microbes in periphytic biofilms implies that they may contain complicated N cycling pathways.…”

Soil Microbial Community Responses to Different Management Strategies in Almond Crop

“…Interactions in the soil are complex, and practices related to tillage, fertilization and irrigation regimes alter the soil microbiota and their related functions [ 22 , 23 ]. The soil microbiome can derive benefits, such as those that improve plant growth (PGPR bacteria), biological control, stress resistance or nutrient cycling [ 24 , 25 ], but also disadvantageous such as phytopathogenic activity. The understanding of how different agricultural practices affect the microbial communities informs us towards more sustainable and/or productive crops.…”

Structural characteristics and diversity of the rhizosphere bacterial communities of wild Fritillaria przewalskii Maxim. in the northeastern Tibetan Plateau

“…Changes in the diversity and composition of rhizosphere microbial communities are often associated with the host plant and its environment, including root secretions, plant growth stages, soil type, and physicochemical properties (Chaparro et al, 2014;Xue et al, 2018;Broadbent et al, 2021). Host plant associated soil microhabitats influence rhizosphere microorganism enrichment (Xiong and Lu, 2022). For example, in recent studies in lilies the rhizosphere microbial community composition differed significantly in different habitats (Xie et al, 2021).…”