Soil Bacteria Research Articles

Spatiotemporal patterns of soil myxomycetes in subtropical managed forests and their potential interactions with bacteria.

Soil myxomycetes are crucial soil protists with important ecological functions. Yet, our understanding of their diversity patterns in managed forests and the interactions with their food is far behind other taxa. This study investigates the spatiotemporal patterns of soil myxomycetes in four northern subtropical managed forest types across seasons and aims to identify assembly processes, main predictors of myxomycete communities, and the potential interactions between myxomycetes and bacteria. Results showed that no significant difference in α diversity of myxomycete communities among forest types was observed, but a significant difference was observed in community structures. Significant differences were observed in α diversity and community structures of myxomycetes among seasons. Deterministic processes in each forest type and season dominated myxomycete community assemblies. Soil physicochemical properties and bacterial communities have a significant direct impact on the myxomycete community, while forest types, seasons, and enzyme activities have an indirect effect. There is a significant synergistic covariation between the soil myxomycete community and bacterial community. The genera of the phyla Acidobacteriota, Actinobacteriota, and Bacteroidota have a strong correlation with the richness of myxomycete genera. Overall, this study provides new insight into the diversity of soil myxomycetes and their influence by bacteria, crucial for myxomycetes ecology.IMPORTANCESoil myxomycetes are an important component of soil protists. Our study revealed for the first time the community structure of soil myxomycetes in managed forests of the northern subtropical regions and systematically investigated the seasonal variation patterns of soil myxomycetes. Meanwhile, we further investigated the potential interactions between soil myxomycetes and bacteria. This study will greatly enhance our understanding of the ecology of soil myxomycetes and their biological roles.

Research on soil bacterial community assembly and function under different straw returning practices in arid and semi-arid agricultural ecosystems over multiple years

IntroductionStraw return has gained attention for its potential to improve soil quality and crop yields, particularly in semi-arid regions like the Tumu Chuan Plain Irrigation Area. Soil bacteria play a crucial role in regulating soil biological processes, and understanding how straw return affects bacterial populations can guide better agricultural management practices.MethodsWe investigated the impact of continuous straw return on soil bacterial communities using 16S rRNA gene sequencing. Four treatments were applied: Farmers’ shallow rotation (CK), straw incorporated with deep tillage (DPR), straw incorporated with subsoiling (SSR), and no-tillage mulching straw return (NTR). Bacterial community structure, metabolic pathways, and assembly mechanisms were analyzed using Bugbase and PICRUSt2 for phenotypic and metabolic pathway predictions.ResultsThe study found that straw return practices significantly altered the relative abundance and life history strategies of bacterial phyla, mainly influenced by soil organic matter (SOM) and enzyme activity. The K-strategist to r-strategist ratio was highest in CK (2.06) and lowest in SSR (1.89). DPR and NTR treatments significantly changed bacterial community structure compared to CK (p < 0.05), resembling SSR. Predictions showed that DPR and NTR enhanced carbohydrate and amino acid metabolism and promoted more stable bacterial networks, with homogenous selection and drift effects. Bacterial aggregation in all treatments was driven by random processes, with varying aggregation levels: CK (20%), DPR (38.6%), SSR (16.5%), and NTR (30.7%).DiscussionThe study demonstrates that continuous straw return practices significantly impact soil bacterial communities. DPR and NTR notably improved microbial diversity, bacterial cooperation, and ecosystem stability. These findings provide valuable insights for sustainable agricultural practices in semi-arid regions, enhancing soil microbial ecology and soil health through strategic straw return.

The role of reactive oxygen, nitrogen and sulphur species in the integration of (a)biotic stress signals in legumes.

Legumes are crops of considerable economic and ecological significance. They are suitable for cultivation in a variety of environments and temperatures. They are able to form a symbiotic relationship with nitrogen-fixing soil bacteria called rhizobia contributing to the enrichment of marginal soils with this essential nutrient, and reduces artificial fertilizer use. Similarly, legumes establish a widespread mutualistic association with soil fungi, involving a reciprocal transfer of nutrients. Global warming is reshaping plant interactions with its environment, exerting profound effects on global agricultural systems. Plants have evolved sensing, signaling, and adaptive molecular mechanisms to respond to (a)biotic stimuli. Reactive oxygen, nitrogen, and sulphur species (RONSS) are key players in stress tolerance mechanisms, and their homeostasis, mainly accomplished by antioxidant enzymes and metabolites, is essential to allow redox signaling while preventing oxidative damage. Here, we review recent findings, highlighting metabolic pathways of RONSS and antioxidants, with emphasis on their functions in signaling and protection in response to (a)biotic constraints in legumes. Special attention is paid to the molecular crosstalk between RONSS in response to multiple stimuli and notably how redox homeostasis adjustment can increase (a)biotic stress tolerance and potentially be exploited to mitigate the negative effects of climate change.

Deciphering key traits and dissemination of antibiotic resistance genes and degradation genes in pharmaceutical wastewater receiving environments.

Deciphering key traits and dissemination of antibiotic resistance genes and degradation genes in pharmaceutical wastewater receiving environments.

The effect of weed control using herbicide on soil bacteria, growth, and yield of sweet corn

Weeds are managed by herbicides, but this can reduce the abundance of soil bacteria. This research aimed to determine the effect of active compounds of herbicides on weeds, the abundance of soil bacteria, growth and yield of sweet corn. The experiment was conducted from June to October 2023 in the fields and Laboratory of Agronomy and Horticulture, Universitas Jenderal Soedirman, Purwokerto. A randomized block design was used, consisting of eight treatments and four replications. The treatments included control (H0); weeding (H1); paraquat (H2); glyphosate (H3); paraquat, atrazine, mesotrione (H4); glyphosate, atrazine, mesotrione (H5); paraquat, atrazine, mesotrione, nicosulfuron (H6); and glyphosate, atrazine, mesotrione, nicosulfuron (H7). Results showed that glyphosate and paraquat, were applied before planting, could suppress weeds on sweet corn until 15 days after planting (DAP). Application of atrazine, mesotrione, and nicosulfuron at 21 DAP can increase the success of weed control observed up to 35 DAP of sweet corn. The application of glyphosate, atrazine, and mesotrione showed the highest values for growth variables (plant height, number, and leaf greenness index) and yield variables (fresh weight, diameter, and length of sweet corn cob). Herbicide decrease abundance of soil bacteria on sweet corn field, from 10.07x10-8 CFU/mL to 9.55x10-8 CFU/mL (total bacteria), 9.53x10-8 CFU/mL to 9.52x10-8 CFU/mL (phosphate solubilizing bacteria), 9.90x10-8 CFU/mL to 9.40x10-8 CFU/mL (Rhizobium) and 9.91x10-8 CFU/mL became 9.78x10-8 CFU/mL (nitrogen fixing bacteria). The total density of phosphate-solubilizing bacteria and nitrogen-fixing bacteria in the application of glyphosate, atrazine, and mesotrione (7.78 CFU/g and 9.52 CFU/g) was greater than control (8.77 CFU/g and 8.15 CFU/g).

Herbivory-induced green leaf volatiles increase plant performance through jasmonate-dependent plant-soil feedbacks.

Plants influence each other chemically by releasing leaf volatiles and root exudates, but whether and how these two phenomena interact remains unknown. Here we demonstrate that volatiles that are released by herbivore-attacked leaves trigger plant-soil feedbacks, resulting in increased performance of different plant species. We show that this phenomenon is due to green leaf volatiles that induce jasmonate-dependent systemic defence signalling in receiver plants, which results in the accumulation of beneficial soil bacteria in the rhizosphere. These soil bacteria then increase plant growth and enhance plant defences. In maize, a cysteine-rich receptor-like protein kinase, ZmCRK25, is required for this effect. In four successive year-field experiments, we demonstrate that this phenomenon can suppress leaf herbivore abundance and enhance maize growth and yield. Thus, volatile-mediated plant-plant interactions trigger plant-soil feedbacks that shape plant performance across different plant species through broadly conserved defence signalling mechanisms and changes in soil microbiota. This phenomenon expands the repertoire of biologically relevant plant-plant interactions in space and time and holds promise for the sustainable intensification of agriculture.

A novel Zn (II)/Cd (II)/Pb (II)-translocating PIB-type ATPase mediates metal resistance in Chryseobacterium sp. strain PMSZPI in metal-enriched soil of uranium ore deposit.

A novel Zn (II)/Cd (II)/Pb (II)-translocating PIB-type ATPase mediates metal resistance in Chryseobacterium sp. strain PMSZPI in metal-enriched soil of uranium ore deposit.

Ampicillin Exposure and Glutathione Deficiency Synergistically Promote Conjugative Transfer of Plasmid-Borne Antibiotic Resistance Genes.

Plasmid-mediated conjugation is an important pathway for the spread of antibiotic resistance genes (ARGs), posing a significant risk to global public health. It has been reported that the conjugative transfer of ARGs could be enhanced by oxidative stress. Whether endogenous glutathione (GSH), a major non-protein thiol compound involved in cellular redox homeostasis, influences conjugative transfer is unknown. In this study, we show that the deletion of the GSH biosynthesis gene gshA and ampicillin exposure synergistically promoted the conjugative transfer of plasmid RP4 bearing multiple ARGs from the soil bacterium Enterobacter sp. CZ-1 to Escherichia coli S17-1λπ in co-culture experiments and to diverse soil bacteria belonging to eight phyla, including some potential human pathogens, in a soil incubation experiment. The deletion of gshA increased ROS generation and cell membrane permeability, and upregulated the expression of the genes involved in intracellular oxidative stress regulation, membrane permeability, plasmid replication, and the SOS response process, especially under ampicillin exposure. These results suggest that endogenous GSH is an important factor affecting the spread of plasmid-borne ARGs. Exposure to antibiotics and environmental stresses that cause a depletion of endogenous GSH invivo are likely to increase the risk of ARG dissemination in the environment.

Short term effects of fire on assembly rules and β-diversity of soil bacteria in Mediterranean soils

Short term effects of fire on assembly rules and β-diversity of soil bacteria in Mediterranean soils

Enhanced sustainable remediation of co-contaminated soil and groundwater with lead and arsenic utilizing the willow-vetiver-permeable reactive barrier system.

Enhanced sustainable remediation of co-contaminated soil and groundwater with lead and arsenic utilizing the willow-vetiver-permeable reactive barrier system.

Organic amendments restore soil biological properties under pesticides application.

Organic amendments restore soil biological properties under pesticides application.

Biofertilization using microalgae-bacteria consortium for phenolic stress mitigation of sprouted barley: Functional genes profiling of soil bacteria

Biofertilization using microalgae-bacteria consortium for phenolic stress mitigation of sprouted barley: Functional genes profiling of soil bacteria

Aromatics valorization to polyhydroxyalkanoate by the ligninolytic bacteria isolated from soil sample.

Aromatics valorization to polyhydroxyalkanoate by the ligninolytic bacteria isolated from soil sample.

Soil resource availability regulates the response of micro-food web multitrophic interactions to heavy metal contamination.

Soil resource availability regulates the response of micro-food web multitrophic interactions to heavy metal contamination.

Quantitative stable isotope probing (qSIP) and cross-domain networks reveal bacterial-fungal interactions in the hyphosphere

BackgroundInteractions between fungi and bacteria have the potential to substantially influence soil carbon dynamics in soil, but we have yet to fully identify these interactions and partners in their natural environment. In this study, we stacked two powerful methods, 13C quantitative stable isotope probing (qSIP) and cross-domain co-occurrence network, to identify interacting fungi and bacteria in a California grassland soil. We used in-field whole plant 13CO2 labeling along with sand-filled ingrowth bags (that trap fungi and hyphae-associated bacteria) to amplify the signal of fungal-bacterial interactions, separate from the bulk soil background.ResultsWe found a total of 54 bacterial ASVs and 9 fungal OTUs that were significantly 13C-enriched. These were saprotrophic and biotrophic fungi, and motile, sometimes predatory bacteria. Among these, 70% of all 13C-enriched bacteria identified were motile. Notably, we detected fungal-bacterial network links between a fungal OTU of the genus Alternaria and several bacterial ASVs of the genera Bacteriovorax, Mucilaginibacter, and Flavobacterium, providing empirical evidence of their direct interactions through C exchange. We observed a strong positive co-occurrence pattern between predatory bacteria of the phylum Bdellovibrionota and fungal OTUs, suggesting the transfer of C across the soil food web.ConclusionsTo date, our ability to associate microbial co-occurrence network patterns with biological interactions is limited, but the incorporation of qSIP allowed us to more precisely detect interacting partners by narrowing in on the taxa that were actively incorporating plant-fixed, fungal-transported labeled substrates. Together, these approaches can help build a mechanistic understanding of the complex nature of fungal-bacterial interactions in soil.

Harnessing Termitarium-Associated Bacillus Species for Biocontrol and Plant Growth Promotion

The prolonged use of artificial fertilizers and agrochemicals damages soil health by reducing water retention, increasing salinity, and disrupting nutrient balance. This highlights the need for eco-friendly alternatives to manage crop diseases. Plant growth promoting rhizobacteria (PGPR) are beneficial soil bacteria that enhance plant growth, suppress pathogens, and restore soil fertility. They produce key compounds like phytohormones, antimicrobial metabolites, and enzymes, making them promising biopesticides and biofertilizers. Additionally, termite mound soil, rich in nutrients and beneficial microorganisms, supports plant growth and crop yield. Bacillus spp. is considered the most suitable PGPR with multiple plant growth promoting (PGP) activities. In this study, 42 soil-inhabiting termitarium bacteria were isolated and screened for their antifungal activity against A. alternata and their plant-growth-promoting activity in vitro. TH5/J showed maximum percentage inhibition of the phyto-pathogen (35.06 %) after 48 hours. CFCF (cell-free culture filtrate) also inhibited A. alternata in vitro. TH5/J produced the highest amount of Indole Acetic Acid (IAA), which supports the PGP in plants. The isolates also tested positively for ammonia and hydrogen cyanide (HCN). TH2/2 and TH5/J showed the maximum PGP activity on the mung bean seeds in vitro. These isolates were identified as belonging to Bacillus spp through biochemical analysis. This study highlights Bacillus spp. from termite mounds as eco-friendly biopesticides and biofertilizers, promoting plant growth of mung beans (Vigna radiata L.) and suppressing A. alternata. It emphasizes termite mound soil as a reservoir of beneficial microbes, offering a sustainable alternative to synthetic agrochemicals.

Wetland restoration suppresses microbial carbon metabolism by altering keystone species interactions

Soil bacteria play a pivotal role in regulating multifaceted functions of terrestrial ecosystems. Unraveling the succession of bacterial communities and the feedback mechanism on soil organic carbon (SOC) dynamics help embed the ecology of microbiome into C cycling model. However, how wetland restoration drives soil bacterial community assembly and species association to regulate microbial C metabolism remains unclear. Here, we investigated soil bacterial diversity, community structure and co-occurrence network, enzyme activities and SOC decomposition in restored wetlands for one, three, and four years from paddy fields in Northeast China. Wetland restoration for three and four years increased taxonomic (richness) and phylogenetic diversities by 2.39–3.96% and 2.13–3.02%, respectively, and increased the relative contribution of nestedness to community dissimilarity, indicating increased richness changed soil bacterial community structure. However, wetland restoration for three and four years decreased the richness index of aerobic Firmicutes by 5.04–5.74% due to stronger anaerobic condition characterized by increased soil Fe2+/Fe3+ from 0.20 to 0.64. Besides, wetland restoration for four years decreased network complexity (characterized by decreased node number by 2.51%, edge number by 9.62%, positive/negative edge number by 6.37%, average degree by 5.74% and degree centralization by 6.34%). Robustness index decreased with the increase of restoration duration, while vulnerability index increased with the increase of restoration duration, indicating that wetland restoration decreased network stability of soil bacterial communities. These results might be because stronger anaerobic condition induced the decrease of aerobic Bacilli richness index in keystone module, thereby reducing positive association within keystone module. Decreased positive species association within keystone module in turn weakened microbial C metabolism by decreasing hydrolase activities from 7.49 to 5.37 mmol kg SOC−1 h−1 and oxidase activities from 627 to 411 mmol kg SOC−1 h−1, leading to the decrease of SOC decomposition rate from 1.39 to 1.08 g C kg SOC−1 during wetland restoration. Overall, our results suggested that although wetland restoration after agricultural abandonment increased soil bacterial diversity, it decreased positive association within Bacilli-dominated keystone module under stronger anaerobic condition, which weakened microbial C metabolism and SOC decomposition.

High-Throughput Tn-Seq Screens Identify Both Known and Novel Pseudomonas putida KT2440 Genes Involved in Metal Tolerance.

Industrial and urban activities release toxic chemical waste into the environment. Pseudomonas putida, a soil bacterium, is known to degrade hydrocarbons and xenobiotics, and possesses numerous genes associated with heavy metal tolerance. Most studies on metal tolerance in P. putida focus solely on over- or underexpressed genes, potentially overlooking important genes with unchanged expression. This study employed a Tn-seq approach to identify the essential genes required for P. putida growth under metal stress. This method enables the identification of mutants with altered fitness in the presence of excess metals. The screen successfully identified a number of known genes implicated in metal resistance, including czcA-1, cadA-3, cadR, and pcoA2, thereby validating the approach. Further analyses using targeted mutagenesis and complementation assays revealed PP_5337 as a putative transcriptional regulator involved in copper tolerance and the two-component system RoxSR (PP_0887/PP_0888) as a key determinant of cadmium tolerance. Additionally, PP_1663 and PP_5002 were identified as contributing to cadmium and cobalt tolerance, respectively. This study provides the first evidence linking these genes to metal tolerance, highlighting gaps in our understanding of metal tolerance mechanisms in P. putida and demonstrating the utility of Tn-seq for identifying novel tolerance determinants.

Plant Growth of the Wild Forage Legume Genista monspessulana is Improved by Bradyrhizobium sp. sv. Genistearum in the Acidic Soils of Northern Morocco.

Genista monspessulana is a wild legume of high fodder value in northern Morocco, where it contributes to livestock feeding, particularly during the lean season. The plant fixes nitrogen in symbiosis with soil bacteria known as rhizobia. To identify and characterize its symbiotic partners, we isolated twenty-two bacteria inhabiting the plant nodules and assessed their phenotypic and genetic diversity as well as their symbiotic efficiency. The 16S rRNA sequences analysis proved that 7 isolates were affiliated with the genus Bradyrhizobium, which significantly improve plant growth under nitrogen deficiency. Based on multi-locus sequence analysis using five different housekeeping genes, three representative strains were selected for further analyses. The phylogenetic analysis of the concatenated sequences of the five genes showed that the closest type strain is Bradyrhizobium canariense LMG 2122265T. The strains nodulate also other Genisteae such as Cytisus villosus and Lupinus luteus besides their host plant. The phylogenetic analysis of the symbiotic nodC gene allowed the assignment of the strains to the symbiovar genistearum. The three strains proved to be very efficient in the fixation of N2 as revealed by their relative and absolute efficiency indexes and may be used as effective individual or mixed inocula, to improve the plant growth in its natural habitat and contribute to soil restoration, and revegetation in Northern Morocco.

Isolation and identification of the lactase (β-galactosidase) from the soil bacterium Weizmannia coagulans and its expression and production in the expression system of Escherichia coli

Isolation and identification of the lactase (β-galactosidase) from the soil bacterium Weizmannia coagulans and its expression and production in the expression system of Escherichia coli