Diversity and functional traits of indigenous soil microbial flora associated with salinity and heavy metal concentrations in agricultural fields within the Indus Basin region, Pakistan

Abstract

Soil salinization and heavy metal (HM) contamination are major challenges facing agricultural systems worldwide. Determining how soil microbial communities respond to these stress factors and identifying individual phylotypes with potential to tolerate these conditions while promoting plant growth could help prevent negative impacts on crop productivity. This study used amplicon sequencing and several bioinformatic programs to characterize differences in the composition and potential functional capabilities of soil bacterial, fungal, and archaeal communities in five agricultural fields that varied in salinity and HM concentrations within the Indus basin region of Pakistan. The composition of bacteria with the potential to fix atmospheric nitrogen (N) and produce the enzyme 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase were also determined. Microbial communities were dominated by: Euryarchaeota (archaea), Actinobacteria, Proteobacteria, Planctomycetota, Firimicutes, Patescibacteria and Acidobacteria (bacteria), and Ascomycota (fungi), and all soils contained phylotypes capable of N-fixation and ACC-deaminase production. Salinity influenced bacterial, but not archaeal or fungal communities. Both salinity and HM altered the relative abundance of many phylotypes that could potentially promote or harm plant growth. These stress factors also appeared to influence the potential functional capabilities of the microbial communities, especially in their capacity to cycle phosphorous, produce siderophores, and act as symbiotrophs or pathotrophs. Results of this study confirm that farms in this region are at risk due to salinization and excessive levels of some toxic heavy metals, which could negatively impact crop and human health. Changes in soil microbial communities and their potential functional capabilities are also likely to affect several critical agroecosystem services related to nutrient cycling, pathogen suppression, and plant stress tolerance. Many potentially beneficial phylotypes were identified that appear to be salt and HM tolerant and could possibly be exploited to promote these services within this agroecosystem. Future efforts to isolate these phylotypes and determine whether they can indeed promote plant growth and/or carry out other important soil processes are recommended. At the same time, identifying ways to promote the abundance of these unique phylotypes either through modifying soil and crop management practices, or developing and applying them as inoculants, would be helpful for improving crop productivity in this region.

PGPB and/or AM Fungi Consortia Affect Tomato Native Rhizosphere Microbiota

“…michiganensis ) [ 48 ]. Rhodocytophaga is a genus often associated with soils with high organic matter content and high salinity [ 49 ]. Skermanella can behave as a mycorrhizal helper bacterium, occurring especially where the number of AM fungal propagules is high [ 50 ].…”

Biofertilizer based on halotolerant microorganisms promotes the growth of rice plants and alleviates the effects of saline stress

“…It is generally acknowledged that soil is identified as salinized when the accumulation of water-soluble salt exceeds 0.1% on the surface or sub-surface of soil or the degree of alkalization exceeds 5% in the alkalized layer of soil (Haj-Amor et al, 2022). The excessive soluble salt contributes to not only reduced absorption of nutrients by crops but also physiological drought or even the death of plants (Marghoob et al, 2022). The soil microorganisms boast not only huge quantity and variety but also utmost adaptability, so that it can survive and play roles in many minor environments that are not suitable for other types of life.…”

Assessment of halotolerant bacterial and fungal consortia for augmentation of wheat in saline soils

“…The expansion of salinity around the globe generally, and in Pakistan particularly, needs special attention . Scientists in countries facing the challenges of agricultural lands deterioration due to salinity are giving special emphasis to the exploration of the indigenous microbial flora for the reclamation of saline soils and to exploit the hidden potential of these microbes for crops augmentation in addition to finding the solution through classical and modern approaches like breeding, gene editing, and development of transgenic crops (Perez-Jimenez and Perez-Tornero, 2020; Marghoob et al, 2022). The present study was conducted to explore the indigenous microbial flora of the Indus basin region of Pakistan and its efficacy to overcome the problems associated with low wheat production by mitigating the adverse effect of salinity, and initial promising results indicated the potential of selected strains for salinity stress alleviation in addition to less dependency on chemical fertilizers.…”

“…Currently, different approaches, e.g., physical and chemical applications, plant breeding, and molecular biology techniques, are being practiced and investigated to tackle this problem, but the outcomes are not satisfactory (Nouri et al, 2017;Ben-Laouane et al, 2020;Perez-Jimenez and Perez-Tornero, 2020;Rani et al, 2022). However, the use of microorganisms is considered to be a more efficient and ecofriendly approach for sustainable agriculture (Mukhtar et al, 2020;Marghoob et al, 2022).…”