Microbial Community Structure and Function in Soils

In permanently submerged coastal wetlands, interactions between biogeochemical processes and microbial communities strongly influence greenhouse gas (GHG) fluxes. To improve our understanding of how redox-driven processes shape GHG dynamics in these ecosystems, we investigated the relationships among iron (Fe) pools, microbial dynamics, and the potential GHG production in subaqueous soils from an interdunal wetland in San Vitale Park (Italy), permanently submerged and affected by seasonal oscillations of the saline water table. Two subaqueous soil columns (WAS-2 and WAS-4), collected from similar settings, were analyzed. Surface layers of WAS-4 showed higher salinity and carbonate content, whereas WAS-2 was characterized by overall higher Fe concentrations. Distinct vertical distributions of organic matter and sulfur (S) were shown along depth. Laboratory incubations revealed that nitrous oxide (N₂O) production was up to ten times higher in WAS-2 than in WAS-4, with peaks in the top 13–14 cm, consistent with more active nitrification-denitrification in surface layers. Methane (CH₄) and carbon dioxide (CO₂) fluxes decreased with depth, reflecting reduced availability of labile carbon. Methanomicrobiales dominated CH₄-producing layers, indicating hydrogenotrophic methanogenesis, while amoA-carrying Nitrosomonadales and Thaumarchaeota, occurred in shallow, organic-rich layers where ammonia supported nitrification and denitrification. Denitrifiers mainly belonged to α- and β-Proteobacteria, consistent with their direct contribution to N₂O peaks. Spearman’s correlations showed N₂O positively correlated to sulfur and labile carbon (C), supporting denitrification under moderately reducing conditions. CH₄ and CO₂ positively correlated with organic C (Corg), total nitrogen (TN), and reactive Fe forms, reflecting redox-mediated microbial respiration and methanogenesis. Trace elements (B, Cr, Cu, Ni) acted as micronutrients or inhibitors depending on concentration. Canonical correspondence analysis indicated depth-structured links among gas fluxes, soil chemistry (Corg, TN, S/C, CaCO₃, P), and microbial distributions: surface layers, rich in labile C and nutrients, supported active bacteria and archaea involved in decomposition, nitrification, and denitrification, whereas deeper layers hosted oligotrophic archaea adapted to inorganic substrates. Overall, Fe pools appeared to be associated with soil processes relevant to GHG dynamics, although the extent of their regulatory role remains uncertain due to potential alterations of redox-sensitive Fe fractions during sample handling. These results contribute to broader efforts to predict GHG emissions in submerged wetland soils by linking redox stratification, inorganic chemistry, and microbial functional groups. Full article

Marine fog is a key non-rainfall water source that sustains microbial activity and transports dissolved nutrients inland, influencing early soil development in hyperarid ecosystems. However, the mechanisms through which sustained fog inputs drive soil surface modification and biocrust formation remain poorly understood. This study evaluated the effects of long-term fog augmentation on soil surface development, biocrust dynamics, and associated microbial communities in the Atacama Desert. We implemented a four-year fog addition field experiment with three sampling times (T0, T24, T48) to assess changes in soil physicochemical properties, biocrust composition, and the integrated multi-diversity of archaea, bacteria, fungi and protist. Sustained fog input transformed bare soils into biological soil crusts, particularly lichen- and moss-dominated stages. This transition was accompanied by increases in soil nitrogen, variations in organic matter accumulation, a shift from alkaline to near-neutral pH, and improvements in soil stability and water retention. Multi-diversity increased over time and was positively associated with ecosystem variables linked to water availability, structural stabilization, and decomposition. These functions, integrated into an ecosystem multifunctionality index, also increased under prolonged fog input, revealing a positive relationship between multifunctionality and multi-diversity. Overall, the results demonstrate that sustained fog input strongly enhances early soil surface development and biocrust establishment, highlighting the ecological importance of marine fog in shaping biodiversity and ecosystem functioning in hyperarid landscapes. Full article

The utilization of the widely distributed saline–alkali lands by planting forage grasses is a hot topic. However, the promotion of plant growth remains a great challenge during the exploration of this stressful soil. While halotolerant bacteria are beneficial for plants against saline–alkali stress, their stable colonization on plant roots should be further strengthened. In this study, we investigated the effect of moss biochar on the root colonization of the exogenous halotolerant Halomonas salifodinae isolated from saline lake sediments. During the incubation with the bacteria, the biochar strongly bound the bacterium and induced biofilm formation on the biochar surface. When the biochar and the bacterium were added into the culturing soil of the forage grass Medicago sativa, the biochar remarkably assisted the root binding and biofilm formation of this bacterium on the plant roots. Under the biochar–bacterium combined treatment, the numbers of total bacteria, halotolerant bacteria, and nitrogen-fixing bacteria increased from 10^5.5 CFU/g soil to 10^7.2 CFU/g soil, from 10^4.5 CFU/g soil to 10^6.1 CFU/g soil, and from 10^4.7 CFU/g soil to 10^6.3 CFU/g soil, respectively. After 30 days of culturing, the biochar and the bacterium in combination increased the plant height from 10.3 cm to 36 cm, and enhanced the accumulation of chlorophyll a, reducing sugars, soluble proteins, and superoxide dismutase in the leaves. Moreover, the combined treatment increased the activity of soil enzymes, including peroxidase, alkaline phosphatase, and urease. Meanwhile, the levels of various cations in the rhizosphere soil were reduced by the combined treatment, e.g., Na⁺, Cu²⁺, Fe²⁺, Mg²⁺, Mn²⁺, etc., indicating an improvement in the soil quality. This study developed the biochar–halotolerant bacterium joint strategy to improve the yield of forage grasses in saline–alkali soil. Full article

Heavy metal(loid) (HM) contamination in soils from smelting activities poses significant environmental and public health risks, as well as disruptions in microbial community dynamics and HM resistance gene profiles. This study investigates the microbial diversity, resistome, and physicochemical properties of soils from the abandoned Avalos smelter in Chihuahua, Mexico. Through soil analyses, we identified elevated concentrations of certain HMs, which pose serious environmental and health hazards. The metagenomic analysis of the microbial community, composed of bacteria, archaea, and fungi, was dominated by genera such as Streptomyces, Bradyrhizobium, Halobaculum, Nitrosocosmicus, Fusarium, and Aspergillus in rhizospheric soil. Furthermore, a diverse array of metal resistance genes (MRGs) were detected, associated with copper, arsenic, iron, lead, cadmium, zinc, and other HMs. Additionally, metagenome-assembled genomes (MAGs) revealed the presence of functional genes linked to HM resistance, providing deeper insights into the ecological roles and metabolic capabilities of microbial taxa. These findings highlight the significant impact of smelting-derived contamination on microbial diversity and functional potential, offering valuable insights for the development of bioremediation strategies in HM-contaminated environments. Full article

Genetic variability in bacterial populations that nodulate Lupinus cosentinii in Tunisia was investigated. Phylogenetic studies of 40 isolates using recA partial sequences categorized them into three clusters within the Bradyrhizobium genus. Twenty-three strains selected from the three clusters were thoroughly examined through housekeeping genes (recA, glnII and rpoB) multilocus sequence analysis (MLSA). Our results showed that 23 representative strains were distributed in five distinct clusters, with 13 strains belonging to Bradyrhizobium canariense BTA-1^T/Bradyrhizobium lupini USDA3051^T (10 strains) and Bradyrhizobium hipponense aSej3^T (three strains) lineages. Interestingly, eight strains occupied a separate position and could belong to two putative novel Bradyrhizobium species. The nodC phylogeny placed the 23 strains within three symbiovars: genistearum (19 strains), lupini (two strains) and, for the first time, the symbiovar cyanophyllae (two strains). Based on the worldwide phylogeography of rhizobial symbionts nodulating lupine (14 species), our results reported that eight species occurred in more than one continent, and six species were specific for one continent, e.g., Bradyrhizobium rifense, Bradyrhizobium diazoefficiens, Phyllobacterium sp. and Devosia sp. were specific to the African continent, the Bradyrhizobium iriomotense/Bradyrhizobium stylosanthis group to America, and Bradyrhizobium valentinum to the European continent. Full article

Rice sustains a large global population, making its sustainable production vital for food security. Alternate wetting-and-drying (AWD) irrigation offers a promising approach to reducing water use in rice paddies but can impact grain yields. Plant growth-promoting rhizobacteria (PGPR) can enhance rice productivity under AWD cultivation conditions. This review explores integrating PGPR into AWD systems, focusing on their mechanisms for promoting growth and water stress resilience. It examines diverse microbial communities, particularly bacteria, and their contributions to nutrient acquisition, root development, and other beneficial processes in rice under fluctuating moisture, as well as the influence of AWD on rice’s structural and physiological development. The challenges and opportunities of AWD are also addressed, along with the importance of bacterial selection and interactions with the native soil microbiome. This synthesizes current research to provide an overview of PGPR’s potential to improve sustainable and productive rice cultivation under AWD. Future studies can leverage powerful tools such as e-DNA and NGS for a deeper understanding of these complex interactions. Full article

Soil is a complex and dynamic ecosystem containing a diverse array of microorganisms, and plays a crucial and multifaceted role in various functions of the ecosystem. Substantial fluctuations in the environmental conditions arise from diverse global changes. The microbial shifts in the soil in concordance with the changing environmental factors, or a combination of these factors, are of high significance. Exploring the contribution of global change drivers to the microbial community to improve the predictions of the response of the microbial community to the functioning of the ecosystem is of prime importance. Promoting the health of soil microorganisms maintains the overall health and fertility of the soil, which in turn supports the health of terrestrial ecosystems and agricultural systems. The current review aims to assemble different abiotic factors or stressors that exist in the environment that affect the microbial community. More focus will be given to one of the stressors—antibiotics, a recent emerging pollutant. The effects on the soil microbial community and the future of soil health due to the presence of antibiotics will be addressed. The scope of the interaction of antibiotics with other pollutants like plastics and heavy metals (HMs) will be examined. Full article