Samiran Banerjee

Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming

BackgroundHarnessing beneficial microbes presents a promising strategy to optimize plant growth and agricultural sustainability. Little is known to which extent and how specifically soil and plant microbiomes can be manipulated through different cropping practices. Here, we investigated soil and wheat root microbial communities in a cropping system experiment consisting of conventional and organic managements, both with different tillage intensities.ResultsWhile microbial richness was marginally affected, we found pronounced cropping effects on community composition, which were specific for the respective microbiomes. Soil bacterial communities were primarily structured by tillage, whereas soil fungal communities responded mainly to management type with additional effects by tillage. In roots, management type was also the driving factor for bacteria but not for fungi, which were generally determined by changes in tillage intensity. To quantify an “effect size” for microbiota manipulation, we found that about 10% of variation in microbial communities was explained by the tested cropping practices. Cropping sensitive microbes were taxonomically diverse, and they responded in guilds of taxa to the specific practices. These microbes also included frequent community members or members co-occurring with many other microbes in the community, suggesting that cropping practices may allow manipulation of influential community members.ConclusionsUnderstanding the abundance patterns of cropping sensitive microbes presents the basis towards developing microbiota management strategies for smart farming. For future targeted microbiota management—e.g., to foster certain microbes with specific agricultural practices—a next step will be to identify the functional traits of the cropping sensitive microbes.

The inorganic nutrient cost of building soil carbon

“ Inorganic nutrients are a hidden cost for sequestering carbon in soil organic matter. ”

Keystone taxa as drivers of microbiome structure and functioning

Microorganisms have a pivotal role in the functioning of ecosystems. Recent studies have shown that microbial communities harbour keystone taxa, which drive community composition and function irrespective of their abundance. In this Opinion article, we propose a definition of keystone taxa in microbial ecology and summarize over 200 microbial keystone taxa that have been identified in soil, plant and marine ecosystems, as well as in the human microbiome. We explore the importance of keystone taxa and keystone guilds for microbiome structure and functioning and discuss the factors that determine their distribution and activities.In this Opinion article, Banerjee et al. explore the importance of microbial keystone taxa and keystone guilds in microbiome structure and functioning, describe challenges in the characterization and manipulation of such taxa, and propose a definition of keystone taxa in microbial ecology.

Novel Screen for Investigating In Situ Rhizosphere Production of the Antibiotic 2,4‐Diacetylphloroglucinol by Bacterial Inocula

Abstract The rhizosphere is a complex zone of multitrophic interactions comprising plant roots, associated bacteria, fungi, and micro‐, meso‐, and macro‐fauna. Of considerable importance in this system is the production of antibiotics by root‐associated or “rhizo” bacteria. This is a widespread phenomenon of which a much‐studied exemplar is the production by pseudomonads of 2,4‐diacetylphloroglucinol (DAPG), known to be effective in the suppression of soil‐borne fungal pathogens. Rapid advances in understanding the molecular and biochemical bases of antibiotic (particularly DAPG) production have been made. However, our understanding of in situ antibiotic production currently lags behind this. There is therefore a need for a rapid soil‐based screen with which to identify antibiotic producers under rhizosphere C‐flow conditions. Here, a novel “rhizocosm,” comprising porous pipe and Rhizon sampler®, was superior to a simple, nonperfusing incubation‐type microcosm with respect to supporting a rhizobacterial inoculum. Its use as a screening tool is illustrated by screening known DAPG‐producing inocula in soil continuously supplied with simulated rhizosphere carbon flow. The DAPG was then extracted from soil using acetone and quantified by high‐performance liquid chromatography (HPLC). Simple sugars (glucose and fructose) stimulated the greatest DAPG production, while glucose with an additional organic or amino acid, or with a signal molecule, resulted in strongly variable DAPG expression.

Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots

Root-associated microbes play a key role in plant performance and productivity, making them important players in agroecosystems. So far, very few studies have assessed the impact of different farming systems on the root microbiota and it is still unclear whether agricultural intensification influences network complexity of microbial communities. We investigated the impact of conventional, no-till and organic farming on wheat root fungal communities using PacBio SMRT sequencing on samples collected from 60 farmlands in Switzerland. Organic farming harboured a much more complex fungal network than conventional and no-till farming systems. The abundance of keystone taxa was the highest under organic farming where agricultural intensification was the lowest. The occurrence of keystone taxa was best explained by soil phosphorus levels, bulk density, pH and mycorrhizal colonization. The majority of keystone taxa are known to form arbuscular mycorrhizal associations with plants and belong to the orders Glomerales, Paraglomerales, and Diversisporales. Supporting this, the abundance of mycorrhizal fungi in roots and soils was also significantly higher under organic farming. To our knowledge, this is the first study to report mycorrhizal keystone taxa for agroecosystems, and we demonstrate that agricultural intensification reduces network complexity and the abundance of keystone taxa in the root microbiota.

Correction to: Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming

Following publication of the original article [1], the authors reported that while the ordination graphs are all correct, the symbols in the legend are wrong.

Linking microbial co-occurrences to soil ecological processes across a woodland-grassland ecotone

Abstract Ecotones between distinct ecosystems have been the focus of many studies as they offer valuable insights into key drivers of community structure and ecological processes that underpin function. While previous studies have examined a wide range of above‐ground parameters in ecotones, soil microbial communities have received little attention. Here we investigated spatial patterns, composition, and co‐occurrences of archaea, bacteria, and fungi, and their relationships with soil ecological processes across a woodland‐grassland ecotone. Geostatistical kriging and network analysis revealed that the community structure and spatial patterns of soil microbiota varied considerably between three habitat components across the ecotone. Woodland samples had significantly higher diversity of archaea while the grassland samples had significantly higher diversity of bacteria. Microbial co‐occurrences reflected differences in soil properties and ecological processes. While microbial networks were dominated by bacterial nodes, different ecological processes were linked to specific microbial guilds. For example, soil phosphorus and phosphatase activity formed the largest clusters in their respective networks, and two lignolytic enzymes formed joined clusters. Bacterial ammonia oxidizers were dominant over archaeal oxidizers and showed a significant association (p < 0.001) with potential nitrification (PNR), with the PNR subnetwork being dominated by Betaproteobacteria. The top ten keystone taxa comprised six bacterial and four fungal OTUs, with Random Forest Analysis revealing soil carbon and nitrogen as the determinants of the abundance of keystone taxa. Our results highlight the importance of assessing interkingdom associations in soil microbial networks. Overall, this study shows how ecotones can be used as a model to delineate microbial structural patterns and ecological processes across adjoining land‐uses within a landscape.