Both Soil Bacteria and Soil Chemical Property Affected the Micropredator Myxobacterial Community: Evidence from Natural Forest Soil and Greenhouse Rhizosphere Soil

The Evolution of Nutrient and Microbial Composition and Maturity During the Composting of Different Plant-Derived Wastes

Composting is an environmentally friendly treatment technology that recycles and sanitizes organic solid waste. This study aimed to assess the evolution of nutrients, maturity, and microbial communities during the composting of different plant-derived wastes. The composting process was conducted over 49 days using three types of plant-derived waste: wheat bran (WB), peanut straw (PS), and poplar leaf litter (PL). This process was examined through physical, chemical, and biological parameters. The results revealed that after 49 days of composting, the three groups experienced significant changes. They were odorless, were insect-free, exhibited a dark brown color, had an alkaline pH value, and had an electrical conductivity (EC) value of less than 4 mS/cm. These characteristics indicated that they had reached maturity. Nutrient content was the most significant factor influencing the degree of humification of the different composting materials, while changes in microbial community diversity were the key driving factors. Significantly, the compost PS, derived from peanut straw, entered the thermophilic phase first, and by the end of composting, it had the lowest organic matter (OM) loss rate (17.4%), with increases in total nitrogen (TN), total phosphorus (TP), and total potassium (TK) in the order of PS > PL > WB. The increase in humus carbon (HSC) content and the humic acid/fulvic acid (HA/FA) ratio followed the order PS > WB > PL. FTIR spectra indicated that PS had greater aromatic characteristics compared to the other samples. The abundance and diversity of bacterial and fungal communities in the compost increased significantly, accompanied by more complex community structures. Crucially, there were no phytotoxic effects in any of the three composting treatments, and the compost PS boasted a high germination index (GI) of 94.79%, with the lowest heavy metal contents. The findings indicate that the compost PS has the highest potential for resource utilization and is suitable for agricultural applications. Our results demonstrate that composting technology for plant-derived waste has the potential to enhance soil fertility and provide a reference for the composting treatment and resource utilization of other plant-derived waste.

Fatty acid metabolism and the oxidative stress response support bacterial predation

Despite growing awareness of their importance in soil ecology, the genetic and physiological traits of bacterial predators are still relatively poorly understood. In the course of a Myxococcus xanthus predator evolution experiment, we identified a class of genotypes leading to enhanced predation against diverse species. RNA-seq analysis demonstrated that this phenotype is linked to the constitutive activation of a predation-specific program. Functional analysis of the mutations accumulated across the evolutionary time in a two-component system and Acyl-CoA-manipulating enzymes revealed the critical roles of fatty acid metabolism and antioxidant gene induction. The former likely adapts the predator to metabolites derived from the prey while the latter protects predatory cells from reactive oxygen species generated by prey cells under stress and released upon lysis during predation. These findings reveal interesting parallels between bacterial predator-prey dynamics and pathogen-host cell interactions.

Medicago truncatula genotype drives the plant nutritional strategy and its associated rhizosphere bacterial communities

Harnessing the plant microbiome through plant genetics is of increasing interest to those seeking to improve plant nutrition and health. While genome-wide association studies (GWAS) have been conducted to identify plant genes driving the plant microbiome, more multidisciplinary studies are required to assess the relationships among plant genetics, plant microbiome and plant fitness. Using a metabarcoding approach, we characterized the rhizosphere bacterial communities of a core collection of 155 Medicago truncatula genotypes along with the plant phenotype and investigated the plant genetic effects through GWAS. The different genotypes within the M. truncatula core collection showed contrasting growth and nutritional strategies but few loci were associated with these ecophysiological traits. To go further, we described its associated rhizosphere bacterial communities, dominated by Proteobacteria, Actinobacteria and Bacteroidetes, and defined a core rhizosphere bacterial community. Next, the occurrences of bacterial candidates predicting plant ecophysiological traits of interest were identified using random forest analyses. Some of them were heritable and plant loci were identified, pinpointing genes related to response to hormone stimulus, systemic acquired resistance, response to stress, nutrient starvation or transport, and root development. Together, these results suggest that plant genetics can affect plant growth and nutritional strategies by harnessing keystone bacteria in a well-connected interaction network.

The genetic basis of predation by myxobacteria

Myxobacteria (phylum Myxococcota) are abundant and virtually ubiquitous microbial predators. Facultatively multicellular organisms, they are able to form multicellular fruiting bodies and swarm across surfaces, cooperatively hunting for prey. Myxobacterial communities are able to kill a wide range of prey microbes, assimilating their biomass to fuel population growth. Their mechanism of predation is exobiotic - hydrolytic enzymes and toxic metabolites are secreted into the extracellular environment, killing and digesting prey cells from without. However, recent observations of single-cell predation and contact-dependent prey killing challenge the dogma of myxobacterial predation being obligately cooperative. Regardless of their predatory mechanisms, myxobacteria have a broad prey range, which includes Gram-negative bacteria, Gram-positive bacteria and fungi. Pangenome analyses have shown that their extremely large genomes are mainly composed of accessory genes, which are not shared by all members of their species. It seems that the diversity of accessory genes in different strains provides the breadth of activity required to prey upon such a smorgasbord of microbes, and also explains the considerable strain-to-strain variation in predatory efficiency against specific prey. After providing a short introduction to general features of myxobacterial biology which are relevant to predation, this review brings together a rapidly growing body of work into the molecular mechanisms and genetic basis of predation, presenting a summary of current knowledge, highlighting trends in research and suggesting strategies by which we can potentially exploit myxobacterial predation in the future.

Characteristics of a lipase ArEstA with lytic activity against drug-resistant pathogen from a novel myxobacterium, Archangium lipolyticum sp. nov

Bacteriolytic myxobacteria are versatile micropredators and are proposed as potential biocontrol agents against diverse bacterial and fungal pathogens. Isolation of new myxobacteria species and exploration of effective predatory products are necessary for successful biocontrol of pathogens. In this study, a myxobacterium strain CY-1 was isolated from a soil sample of a pig farm using the Escherichia coli baiting method. Based on the morphological observation, physiological test, 16S rRNA gene sequence, and genomic data, strain CY-1 was identified as a novel species of the myxobacterial genus Archangium, for which the name Archangium lipolyticum sp. nov. was proposed. Subsequent predation tests indicated that the strain efficiently lysed drug-resistant pathogens, with a higher predatory activity against E. coli 64 than Staphylococcus aureus GDMCC 1.771 (MRSA). The lysis of extracellular proteins against ester-bond-containing substrates (tributyrin, tween 80, egg-yolk, and autoclaved drug-resistant pathogens) inspired the mining of secreted predatory products with lipolytic activity. Furthermore, a lipase ArEstA was identified from the genome of CY-1, and the heterologously expressed and purified enzyme showed bacteriolytic activity against Gram-negative bacteria E. coli 64 but not against Gram-positive MRSA, possibly due to different accessibility of enzyme to lipid substrates in different preys. Our research not only provided a novel myxobacterium species and a candidate enzyme for the development of new biocontrol agents but also reported an experimental basis for further study on different mechanisms of secreted predatory products in myxobacterial killing and degrading of Gram-negative and Gram-positive preys.

Diversity and Functional Distribution Characteristics of Myxobacterial Communities in the Rhizosphere of Tamarix chinensis Lour in Ebinur Lake Wetland, China

Soil salinity and desertification are seriously threatening the ecological environment of Ebinur Lake Wetland. Myxobacteria are the main soil microbes in this wetland. However, it is still unclear if the myxobacterial community structure and diversity can improve the ecological environment of Ebinur Lake Wetland by regulating soil nutrient cycling. Therefore, based on high-throughput sequencing of 16SrRNA gene technology, the composition, function, and diversity of the myxobacterial community in the rhizosphere of Tamarix chinensis Lour in Ebinur Lake Wetland were studied. Rhizosphere soil samples were collected from 10 sampling sites (S1, S2, S3, S4, S5, S6, S7, S8, S9, and S10) for three months (April, July, and October) to explore the main biotic and abiotic factors affecting the diversity and functions of myxobacterial communities. The results revealed that diversity of myxobacterial communities was mainly influenced by the seasons. The diversity of myxobacterial communities was significantly higher in the month of July, as compared to April and October. FAPROTAX functional prediction revealed that, in addition to predation or parasitic functions, myxobacteria were mainly involved in ecological functions, such as nitrite respiration, nitrite ammonification, and nitrogen respiration. The Spearman correlation analysis of the diversity and function of myxobacteria and bacteria showed that there were significant positive correlations between myxobacteria diversity, function, and bacterial diversity. The co-occurrence analysis of myxobacteria and bacterial networks showed that over time, myxobacteria interacted differently with different bacterial networks and jointly regulated the microbial community in the rhizosphere of Tamarix chinensis Lour through predation or cooperation. The redundancy analysis of soil physicochemical factors as well as the myxobacterial community showed that electrical conductivity, exchangeable calcium, and exchangeable potassium were the most important abiotic factors affecting the diversity, structure, and function of the myxobacterial community. These results reveal that myxobacteria may play important roles in degrading nitrogen compounds and regulating the activity of soil microorganisms. This study provides theoretical support for the ecological restoration of Ebinur Lake Wetland and lays the foundation for the future development and utilization of myxobacteria resources.

Phylogenetic diversity of stochasticity-dominated predatory myxobacterial community drives multi-nutrient cycling in typical farmland soils

Predatory myxobacteria are keystone taxa in the soil microbial food web that potentially regulate soil microbial community structure and ecosystem functions. However, little is known about the community assembly processes of myxobacteria in typical farmland soils over large geographic scales, in addition to their relationship with soil multi-nutrient cycling. Here, we used high-throughput sequencing techniques and phylogenetic null modeling analysis to investigate the distribution patterns and assembly processes of myxobacteria communities, in addition to interactions between myxobacteria communities and soil multi-nutrient cycling. Anaeromyxobacter (28.5 %) and Haliangium (19.6 %) were the dominant myxobacteria genera in all samples, and myxobacteria community similarities exhibited distinct distance-decay relationships. Stochastic processes (~77.8 %) were the dominant ecological processes driving the assembly of predatory myxobacteria communities over large geographical scales and under three fertilization regimes. Myxobacteria community structure was influenced by geographic factors (location and climate), soil factors (soil pH, soil organic carbon, total nitrogen, and total potassium), and fertilization, with myxobacteria community assembly being more sensitive to geographic factors. Organic-inorganic combined fertilization (NPKM) increased the proportions of deterministic processes in myxobacteria community assembly. Moreover, myxobacteria community assembly and diversity were closely associated with soil multi-nutrient cycling. Hence, myxobacteria phylogenetic α-diversity represented by NTI index is a potential bioindicators for soil multi-nutrient cycling. Overall, our findings comprehensively reveal the mechanisms of assembly of myxobacteria communities in soils over large geographic scales, and provide a theoretical basis for further research on the role of predatory bacteria on soil nutrient cycling in agro-ecosystems.

Concepts and conjectures concerning predatory performance of myxobacteria

Myxobacteria are excellent model organisms for investigation of predator-prey interactions and predatory shaping of microbial communities. This review covers interdisciplinary topics related to myxobacterial predation and provides current concepts and challenges for determining predatory performance. Discussed topics include the role of specialized metabolites during predation, genetic determinants for predatory performance, challenges associated with methodological differences, discrepancies between sequenced and environmental myxobacteria, and factors that influence predation.

Community Profile and Drivers of Predatory Myxobacteria under Different Compost Manures

Myxobacteria are unique predatory microorganisms with a distinctive social lifestyle. These taxa play key roles in the microbial food webs in different ecosystems and regulate the community structures of soil microbial communities. Compared with conditions under conventional management, myxobacteria abundance increases in the organic soil, which could be related to the presence of abundant myxobacteria in the applied compost manure during organic conditions. In the present study,16S rRNA genes sequencing technology was used to investigate the community profile and drivers of predatory myxobacteria in four common compost manures. According to the results, there was a significant difference in predatory myxobacteria community structure among different compost manure treatments (p < 0.05). The alpha-diversity indices of myxobacteria community under swine manure compost were the lowest (Observed OTU richness = 13.25, Chao1 = 14.83, Shannon = 0.61), and those under wormcast were the highest (Observed OTU richness = 30.25, Chao1 = 31.65, Shannon = 2.62). Bacterial community diversity and Mg²⁺ and Ca²⁺ concentrations were the major factors influencing the myxobacteria community under different compost manure treatments. In addition, organic carbon, pH, and total nitrogen influenced the community profile of myxobacteria in compost manure. The interaction between myxobacteria and specific bacterial taxa (Micrococcales) in compost manure may explain the influence of bacteria on myxobacteria community structure. Further investigations on the in-situ community profile of predatory myxobacteria and the key microorganism influencing their community would advance our understanding of the community profile and functions of predatory microorganisms in the microbial world.

The soil microbial food web revisited: Predatory myxobacteria as keystone taxa?

Trophic interactions are crucial for carbon cycling in food webs. Traditionally, eukaryotic micropredators are considered the major micropredators of bacteria in soils, although bacteria like myxobacteria and Bdellovibrio are also known bacterivores. Until recently, it was impossible to assess the abundance of prokaryotes and eukaryotes in soil food webs simultaneously. Using metatranscriptomic three-domain community profiling we identified pro- and eukaryotic micropredators in 11 European mineral and organic soils from different climes. Myxobacteria comprised 1.5-9.7% of all obtained SSU rRNA transcripts and more than 60% of all identified potential bacterivores in most soils. The name-giving and well-characterized predatory bacteria affiliated with the Myxococcaceae were barely present, while Haliangiaceae and Polyangiaceae dominated. In predation assays, representatives of the latter showed prey spectra as broad as the Myxococcaceae. 18S rRNA transcripts from eukaryotic micropredators, like amoeba and nematodes, were generally less abundant than myxobacterial 16S rRNA transcripts, especially in mineral soils. Although SSU rRNA does not directly reflect organismic abundance, our findings indicate that myxobacteria could be keystone taxa in the soil microbial food web, with potential impact on prokaryotic community composition. Further, they suggest an overlooked, yet ecologically relevant food web module, independent of eukaryotic micropredators and subject to separate environmental and evolutionary pressures.

Soil Microbial Indicators within Rotations and Tillage Systems

Recent advancements in agricultural metagenomics allow for characterizing microbial indicators of soil health brought on by changes in management decisions, which ultimately affect the soil environment. Field-scale studies investigating the microbial taxa from agricultural experiments are sparse, with none investigating the long-term effect of crop rotation and tillage on microbial indicator species. Therefore, our goal was to determine the effect of rotations (continuous corn, CCC; continuous soybean, SSS; and each phase of a corn-soybean rotation, Cs and Sc) and tillage (no-till, NT; and chisel tillage, T) on the soil microbial community composition following 20 years of management. We found that crop rotation and tillage influence the soil environment by altering key soil properties, such as pH and soil organic matter (SOM). Monoculture corn lowered pH compared to SSS (5.9 vs. 6.9, respectively) but increased SOM (5.4% vs. 4.6%, respectively). Bacterial indicator microbes were categorized into two groups: SOM dependent and acidophile vs. N adverse and neutrophile. Fungi preferred the CCC rotation, characterized by low pH. Archaeal indicators were mainly ammonia oxidizers with species occupying niches at contrasting pHs. Numerous indicator microbes are involved with N cycling due to the fertilizer-rich environment, prone to aquatic or gaseous losses.