Harnessing soil bacteria and their benefits for sustainable agriculture with changing climate.

Soil bacteria contribute effectively to key biogeochemical reactions in the soil rhizosphere. They support plants in the rhizosphere to adapt quickly to changing climatic conditions. Differences in root exudates, trace gas chemistry, chemical compounds and nutrient exchange contribute to the recruitment of diverse microorganisms by plant roots. This review highlights the importance of characterizing novel microorganisms to support sustainable agricultural practices. We discuss about tools for characterizing microbes and agricultural practices that influence microbial diversity, and have reviewed how microorganisms may have important but unidentified roles in climate change. Beneficial microbes could improve the turnover of carbon, nitrogen, phosphorus and other minerals thereby avoiding the use of chemical inputs, which are not only causing serious environmental harm but also pose danger to human and animal health.

Enhancing Cucurbita pepo Growth, Productivity, and Fruit Quality using Bacilli Strains and Cyanobacteria Treatments

Two successful field experiments were carried out during 2020and 2021 growing seasons to evaluate the effect of bio fertilizers; Bacillus amyloliquifaciens (BA), Bacillus megaterium (BM) and cyanobacteria inoculation on the vegetative growth, growth parameters and plant chemical content of Cucurbita pepo (Squash) crop. The study of mixed inoculation with both Bacillus strains, and cyanobacteria was found to improve vegetative growth, plant chemical contents and positive microbial activity in the soil Rhizosphere in comparison to un-inoculated plants. Soil available nutrients (N and K) increased significantly with BA and BM combined with cyanobacteria while available phosphorus gave most increase with BM.

Advances in screening approaches for the development of microbial bioprotectants to control plant diseases

The success of a biological control programme depends on the isolation and selection of antagonists. There is an enormous diversity of culturable microbial species in the soil, rhizosphere, phylloplane, spermosphere and carposphere, which can be used in the isolation and selection of antagonists. The structures of fungal plant pathogens concerned with survival and infection may also be sources of antagonists. Although non-culturable microorganisms and microbiome-based strategies have great potential for development as commercial products in disease control, more knowledge is needed to understand the mechanisms involved in interactions between plants and complex microbial communities. Methods of isolation and selection of the most commercially exploited groups of antagonists and their advantages and disadvantages are discussed in this chapter as well as those of non-traditional antagonists. Finally, possible strategies for engineering the soil and host microbiome to actively promote plant protection against pathogens are discussed.

Anatomical Boundaries in Plant Roots Form Important Barriers for Selection of the Soil Microbiome

Background The microbiome in plant-soil systems has a significant influence in promoting plant growth. The extent of selectivity that the plant exerts on the microbiome in the continuum of internal plant tissues is not well understood. This study analysed the root microbiome of a legume, Melilotus officinalis (L.) Pall., sweet clover, and focused on dynamic shifts in the microbial community structure through the niches of bulk soil, rhizosphere, periderm, phloem and xylem, and further examined the effects of environmental factors, root exudates and root cell wall development on the microbiome assemblages in different root compartments.ResultsYoung and mature plants were sampled at 24 field sites and the microbial communities in different niches from bulk soil and rhizosphere through to root compartments were analysed by 16S rRNA gene sequencing. The microbiome composition changed from periderm to phloem to a greater extent than across other boundaries (0.95 vs 0.71 based Bray–Curtis distance). Variation in microbiome composition was associated with geographic distance and soil properties for the bulk soil, rhizosphere and periderm niches. The composition of root exudate compounds were correlated with the rhizosphere microbiome assemblages in mature and young plants. The endophyte communities that occupied the phloem and xylem were most conserved and were independent of growing environments and root exudation. Symbiotic rhizobia able to nodulate M. officinalis were prominent colonisers of the periderm (~15%) and xylem (~6.2%), but were only a minor component in other soil-related niches (0.1%-2.5%). In xylem tissues, endophyte diversity was correlated with the total cell wall and lignin content across the sampled sites (r=0.29-0.62). Conclusions Our results demonstrate that selection of microbiome constituents occurs at different boundaries through bulk soil, rhizosphere, periderm, phloem and xylem, and is especially strong across the periderm boundary. The conserved endophyte community in the innermost tissues (phloem and xylem) was identified, and will be advantageous to the development of specific beneficial microbial inoculants.

Effect of Short-Term Low-Nitrogen Addition on Carbon, Nitrogen and Phosphorus of Vegetation-Soil in Alpine Meadow

As one of the nitrogen (N) limitation ecosystems, alpine meadows have significant effects on their structure and function. However, research on the response and linkage of vegetation-soil to short-term low-level N deposition with rhizosphere processes is scant. We conducted a four level N addition (0, 20, 40, and 80 kg N ha−1 y−1) field experiment in an alpine meadow on the Qinghai-Tibetan Plateau (QTP) from July 2014 to August 2016. We analyzed the community characteristics, vegetation (shoots and roots), total carbon (TC), nutrients, soil (rhizosphere and bulk) properties, and the linkage between vegetation and soil under different N addition rates. Our results showed that (i) N addition significantly increased and decreased the concentration of soil nitrate nitrogen (NO3−-N) and ammonium nitrogen, and the soil pH, respectively; (ii) there were significant correlations between soil (rhizosphere and bulk) NO3−-N and total nitrogen (TN), and root TN, and there was no strong correlation between plant and soil TC, TN and total phosphorus, and their stoichiometry under different N addition rates. The results suggest that short-term low-N addition affected the plant community, vegetation, and soil TC, TN, TP, and their stoichiometry insignificantly, and that the correlation between plant and soil TC, TN, and TP, and their stoichiometry were insignificant.

Indirect Effects of the Herbicide Glyphosate on Plant, Animal and Human Health Through its Effects on Microbial Communities

The herbicide glyphosate interferes with the shikimate pathway in plants and in major groups of microorganisms impeding the production of aromatic amino acids. Glyphosate application on plants results in a slow death, accelerated by reduced resistance to root pathogens. Extensive glyphosate use has resulted in increasing residues in soil and waterways. Although direct glyphosate effects on animals are limited, major concerns have arisen about indirect harmful side effects. In this paper, we focus on indirect effects of sublethal concentrations of glyphosate on plant, animal and human health due to shifts in microbial community compositions in successive habitats. Research results of glyphosate effects on microbial communities in soil, rhizosphere and animal guts have been contradictory due to the different integration levels studied. Most glyphosate studies have tested short-term treatment effects on microbial biomass or general community composition at higher taxonomic levels in soil, rhizosphere or animal intestinal tracts, and found little effect. More detailed studies showed reductions in specific genera or species as well as biological processes after glyphosate application. Plant growth promoting rhizobacteria and beneficial intestinal bacteria often are negatively affected, while pathogenic bacteria and fungi are enhanced. Such shifts in microbial community composition have been implicated in enhanced susceptibility of plants to Fusarium and Rhizoctonia, of birds and mammals to toxic Clostridium and Salmonella species, and of bees to Serratia and Deformed Wing Virus. In animals and humans, glyphosate exposure and concentrations in urine have been associated with intestinal diseases and neurological as well as endocrine problems, but cause-effect relationships need to be determined in more detail. Nevertheless, outbreaks of several animal and plant diseases have been related to glyphosate accumulation in the environment. Long-term glyphosate effects have been underreported, and new standards will be needed for residues in plant and animal products and the environment.

Plant–Microbe Interaction: Aboveground to Belowground, from the Good to the Bad

Soil health and fertility issues are constantly addressed in the agricultural industry. Through the continuous and prolonged use of chemical heavy agricultural systems, most agricultural lands have been impacted, resulting in plateaued or reduced productivity. As such, to invigorate the agricultural industry, we would have to resort to alternative practices that will restore soil health and fertility. Therefore, in recent decades, studies have been directed towards taking a Magellan voyage of the soil rhizosphere region, to identify the diversity, density, and microbial population structure of the soil, and predict possible ways to restore soil health. Microbes that inhabit this region possess niche functions, such as the stimulation or promotion of plant growth, disease suppression, management of toxicity, and the cycling and utilization of nutrients. Therefore, studies should be conducted to identify microbes or groups of organisms that have assigned niche functions. Based on the above, this article reviews the aboveground and below-ground microbiomes, their roles in plant immunity, physiological functions, and challenges and tools available in studying these organisms. The information collected over the years may contribute toward future applications, and in designing sustainable agriculture.