Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach

Biochar (BC) application is widely recognized as a promising strategy for enhancing soil fertility; however, its lasting effects on microbial communities in aeolian sandy soils of semi-arid regions remain poorly understood. To fill this knowledge gap, we conducted a field experiment to evaluate long-term changes in soil properties and microbial community structure in a buckwheat cropping system, 4 years after a single application of biochar (BC) at rates of 0 (BC0), 20 (BC1), 40 (BC2), and 60 (BC3) Mg ha-1 in aeolian sandy soils of Inner Mongolia, China. Results revealed significant improvements in soil pH, moisture content, organic carbon (SOC), and available nutrients, as well as microbial biomass and enzyme activity, particularly at higher BC application rates (BC2 and BC3). SOC increased by 9.42% (BC2) and 14.13% (BC3). BC application altered microbial community composition, with minimal effects on bacterial diversity but reduced fungal diversity. Enhanced soil C and N cycling was linked to shifts in key microbial genera, while relative abundances of potential pathogens such as Fusarium and Nothophoma declined by up to 58 and 77%, respectively. Mantel tests confirmed significant correlations between shifts in microbial diversity and community composition and changes in soil properties, with particularly strong associations for fungal diversity related to SOC (r = 0.50, p < 0.001) and microbial biomass carbon (SMC; r = 0.43, p < 0.001). Redundancy analysis further revealed that bacterial communities were significantly associated (p < 0.05) with pH, microbial biomass nitrogen (SMN), and invertase activity, while fungal communities were linked to pH, microbial biomass phosphorus (SMP), and urease activity. This study underscores the potential of biochar to enhance soil health by improving soil fertility, reshaping microbial community composition, and suppressing soil-borne pathogens, particularly at higher application rates. These findings provide valuable insights for the reclamation of degraded sandy soils in semi-arid regions on a global scale.

The mining industry in China plays a pivotal role in economic development but also leads to severe environmental issues, particularly heavy metal pollution in soils. Heavy metal pollution significantly impacts soil microbial communities due to its persistence and long-term residual effects. We assessed changes in microbial diversity, community structure, and assembly mechanisms in selenium-impacted soils. This study investigates the impacts of selenium (Se) and other heavy metals on soil microbial communities in selenium-rich mining areas using full-length 16S rRNA gene sequencing. Our results showed that Se and other heavy metal contamination significantly altered microbial community composition, favoring metal-tolerant phyla such as Proteobacteria, Actinobacteriota and Firmicutes, while reducing the abundance of sensitive groups like Acidobacteriota and Chloroflexi. Microbial diversity decreased as Se and other heavy metal concentrations increased. Mantel test analysis revealed that soil total potassium (TK), soil organic carbon, total nitrogen, and several other metals, including zinc, niobium, titanium (Ti), manganese, rubidium, barium, potassium, cobalt, gallium (Ga), Se, chromium (Cr), vanadium, and copper were significantly and positively correlated with microbial community composition across all soil samples. Random forest analysis showed that soil TK and multiple elements [Cr, Ti, nickel (Ni), Ga and Se] were the most important predictors of bacterial diversity, emphasizing the role of multiple elements in shaping microbial communities. Co-occurrence network analysis revealed that Se and other heavy metal contamination reduced network complexity and stability, with high Se-contaminated soils exhibiting fragmented microbial networks. Community assembly was primarily driven by drift in control soils, whereas dispersal limitation became more prominent in Se-contaminated soils due to heavy metal toxicity. These findings highlight the ecological consequences of heavy metal pollution on microbial communities and offer valuable insights for effective soil management and remediation strategies.

Soil salinization is one main environmental factor restricting plant growth and agricultural productivity. However, phytoremediation is one of the important means to improve saline-alkali soil by planting halophytes or salt-tolerant plants. In order to study whether there are differences among soil microorganisms in different phytoremediation, the effects of four plants, including alfalfa (MX), oil sunflower (YK), maize (YM) and ryegrass (HMC) on soil physicochemical properties, enzyme activity and microbial community diversity and composition were investigated in this study and the relationships between microbial community structure and soil physicochemical properties, enzyme activity were analyzed. The results showed that all plants treatments significantly decreased pH, TS (total saltinity) and BD (bulk density), while increased OM (organic matter), TN (total nitrogen), AN (available nitrogen), TP (total phosphorus), AP (available phosphorus), TK (total potassium) and TPOR (total porosity), and the number of nitrite bacteria reduced by planting at the same time. Except for YM, other treatments significantly increased the number of nitrifying and denitrifying bacteria compared with CK, while only YK increased that of fungi. Additionally, all plants increased the activity of nitrite reductase and decreased that of urease. More interestingly, plants treatments shifted microbial community compositions, and only YM significantly decreased the bacterial diversity and increased the fungal diversity. Redundancy analysis suggested that TK, pH, BD, TS, AN, OM and nitrite reductase, lignin peroxidase were the key environmental factors that shaped the bacterial community structure, while that of fungi was mainly driven by OM, nitrite reductase, urease and lignin peroxidase. The results indicated that MX and YM are the best choice for remediation of saline-alkali soil. These data can provide certain theoretical basis for the further restoration of saline-alkali land. HIGHLIGHTS The effects of different phytoremediation on microbial diversity and community structure were different. Phytoremediation can significantly decreased pH, TS and BD, while increased OM, TN, AN, TP, AP, TK and TPOR in saline-alkali soil. All plants increased the activity of nitrite reductase and decreased the activity of urease.

Currently, characterization of soil microbial communities relies heavily on the use of molecular approaches. Independently of the approach used, soil DNA extraction is a crucial step, and success of downstream procedures will depend on how well DNA extraction was performed. Often, studies describing and comparing soil microbial communities are based on a single DNA extraction, which may not lead to a representative recovery of DNA from all organisms present in the soil. The use of successive DNA extractions might improve soil microbial characterization, but the benefit of this approach has only been limitedly studied. To determine whether successive DNA extractions of the same soil sample would lead to different observations in terms of microbial abundance and community composition, we performed three successive extractions, with two widely used commercial kits, on a range of clay and sandy soils. Successive extractions increased DNA yield considerably (1–374%), as well as total bacterial and fungal abundances in most of the soil samples. Analysis of the 16S and 18S ribosomal RNA genes using 454-pyrosequencing, revealed that microbial community composition (taxonomic groups) observed in the successive DNA extractions were similar. However, successive DNA extractions did reveal several additional microbial groups. For some soil samples, shifts in microbial community composition were observed, mainly due to shifts in relative abundance of a number of microbial groups. Our results highlight that performing successive DNA extractions optimize DNA yield, and can lead to a better picture of overall community composition.

There is growing interest in understanding the linkages between above- and belowground communities, and very little is known about these linkages in tropical systems. Using an experimental site at La Selva Biological Station, Costa Rica, we examined whether plant diversity, plant community composition, and season influenced microbial communities. We also determined whether soil characteristics were related to differences in microbial communities. Phospholipid fatty acid (PLFA) composition revealed that microbial community composition differed across a plant diversity gradient (plots contained 1, 3, 5, or over 25 species). Plant species identity also was a factor influencing microbial community composition; PLFA composition significantly varied among monocultures, and among three-species combinations that differed in plant species composition. Differences among treatments within each of these comparisons were apparent in all four sampling dates of the study. There was no consistent shift in microbial community composition between wet and dry seasons, although we did see significant changes over time. Of all measured soil characteristics, soil C/N was most often associated with changes in microbial community composition across treatment groups. Our findings provide evidence for human alteration of soil microbial communities via the alteration of plant community composition and diversity and that such changes are mediated in part by changes in soil carbon quality.

Microbiological monitoring of samples collected from oilfield operations is crucial for understanding microbial impacts on metal infrastructure. As many oilfields and related infrastructure are in remote locations, the time between sample collection, shipping to laboratory and sample processing for microbiological analysis can vary from days to weeks. Hence, robust sample handling and preservation methodology to arrest microbiological activity at the time of sample collection is needed. To identify the best preservation methodologies that can be adopted for solids, oily sludge samples were collected twice from the nose of the same pig trap during a routine pipeline pigging operation of a crude oil transmission pipeline over a span of two years. Samples were chemically preserved at the time of sample collection (with different alcohols or commercially available nucleic acid preservation reagents) or remained unpreserved, and all samples were stored either at 4°C or at room temperature following collection. Samples were assessed using 16S rRNA gene sequencing to determine microbial community composition at day 0 (time of sample collection) and at different intervals for up to 50 days of storage, and comparisons in microbial community composition were made to the day 0 results. A substantial shift in microbial community composition was observed in samples that were not chemically preserved or not kept cold at 4°C in as little as 7 days following sludge collection. In addition, greater microbial diversity and community shift was observed in samples kept at room temperature compared to cold storage. Chemical preservation reagents showed varying efficacies at preserving microbial community composition with increased lengths of storage. These results emphasize the need for careful sample preservation and handling of sludge samples for accurate monitoring of microbial communities, an analysis that can play a pivotal role in the early identification of potentially corrosive microorganisms during the routine inspection of pipelines.

Effects of plant and influent C:N:P ratio on microbial diversity in pilot-scale constructed wetlands

Lonar Lake is a hypersaline and hyperalkaline soda lake and the only meteorite impact crater in the world situated in basalt rocks. Although culture-dependent studies have been reported, a comprehensive understanding of microbial community composition and structure in Lonar Lake remains elusive. In the present study, microbial community structure associated with Lonar Lake sediment and water samples was investigated using high-throughput sequencing. Microbial diversity analysis revealed the existence of diverse, yet largely consistent communities. Proteobacteria (30%), Actinobacteria (24%), Firmicutes (11%), and Cyanobacteria (5%) predominated in the sequencing survey, whereas Bacteroidetes (1.12%), BD1-5 (0.5%), Nitrospirae (0.41%), and Verrucomicrobia (0.28%) were detected in relatively minor abundances in the Lonar Lake ecosystem. Within the Proteobacteria phylum, the Gammaproteobacteria represented the most abundantly detected class (21–47%) within sediment samples, but only a minor population in the water samples. Proteobacteria and Firmicutes were found at significantly higher abundance (p ≥ 0.05) in sediment samples, whereas members of Actinobacteria, Candidate division TM7 and Cyanobacteria (p ≥ 0.05) were significantly abundant in water samples. Compared to the microbial communities of other hypersaline soda lakes, those of Lonar Lake formed a distinct cluster, suggesting a different microbial community composition and structure. Here we report for the first time, the difference in composition of indigenous microbial communities between the sediment and water samples of Lonar Lake. An improved census of microbial community structure in this Lake ecosystem provides a foundation for exploring microbial biogeochemical cycling and microbial function in hypersaline lake environments.

Using landscape and depth gradients to decouple the impact of correlated environmental variables on soil microbial community composition

Elevation explains variation in soil microbial diversity and community composition under experimental warming and fertilization treatments in mountain meadows

PurposeMicroorganisms are important in tobacco aging. These are used to improve the quality of tobacco leaves after threshing and redrying. However, the response of microbial community to the storage environment and time during the tobacco aging process has been less explored. This study aimed to characterize the dynamic changes in microbial community composition and diversity in tobacco leaf samples.MethodsIn this study, 16S and ITS rRNA gene amplicon sequencing techniques were used to characterize the composition, diversity, and co-occurrence of the microbial community in tobacco leaves stored in two different cities during the 24-month aging. Furthermore, the activities of several enzymes were measured spectrophotometrically, and the correlation between the microbiota and enzyme activity was analyzed by network analysis.ResultsShannon diversity and Chao richness of bacterial communities gradually increased during the first 18 months, whereas those of the fungal community decreased. The relative abundance of Proteobacteria decreased, whereas that of Actinobacteria and Bacteroidetes increased. The proportion of Ascomycota gradually increased during the first 18 months and then rapidly decreased, whereas the proportion of Basidiomycota exhibited a completely opposite pattern. The change in the composition of bacterial community and dominant genera in leaves was not significant between Guiyang city and Maotai city storerooms, but that in the fungal community was significant. The network analysis revealed that fungal networks were more complex and compact than bacterial networks, and a strong negative correlation existed between bacteria and fungi. Moreover, the bacterial microbiome showed a strong positive association with amylase activity, while the fungal microbiome positively correlated with cellulase activity.ConclusionsThis study demonstrated a significant spatiotemporal heterogeneity in the composition of the microbial community during tobacco aging and highlighted the possible influence of the interactions and enzyme activity on microbial diversity and composition. The findings provided a scientific basis for using microorganisms to regulate and control tobacco aging.

The multi-national in situ Materials Corrosion Test (MaCoTe), being conducted at the Grimsel Test Site in Switzerland, assesses the stability of bentonite as it may be utilized within deep geological repositories (DGRs), which are proposed for the safe, long-term disposal of used nuclear fuel. This experiment provides an opportunity for long-term assessments of changes in microbial communities associated with compacted subsurface bentonite samples exposed to a natural groundwater. Leveraging samples from MaCoTe, herein, we report temporal data for the abundance and community composition of microorganisms associated with compacted bentonite samples emplaced over 7 years under in situ subsurface conditions. Phospholipid fatty acid analysis, 16S rRNA gene quantification and sequencing, cultivation, and natural organic matter analyses all indicated no significant changes for microbial community abundances associated with inner layers of bentonite samples over the 7 years. While microbial abundances did not change in the inner layers, the PLFA data suggest potential changes in microbial community composition and could also indicate prolonged microbial turnover rates. Overall, the results support microbial stability in compacted bentonite exposed to DGR-like conditions for at least 7 years.IMPORTANCELong-term assessments of changes in microbial activity in compacted low-biomass bentonite systems analogous to deep geological repositories (DGRs) are critical to test conditions for stable engineered bentonite barrier components. This study assesses long-term temporal changes in microbial communities of compacted bentonites exposed to natural groundwater. It offers 7-year data that indicate stability of bentonite-based materials intended for use in engineered barrier systems of a DGR for the safe, long-term disposal of used nuclear fuel, with wider implications for microbial persistence in a deep subsurface environment.

Soil microorganisms are greatly affected by their microenvironment. To reveal the influence of different land use patterns on the composition and diversity of soil bacterial and fungal communities, this study analyzed microbial (bacteria and fungi) community composition and diversity under different land use patterns (vegetable land, wasteland, woodland, cultivated land) based on 16S rRNA, 18S rRNA, and high-throughput sequencing method in the Taojia River Basin. Spearman analysis and redundancy analysis (RDA) were used to explore the correlation between soil physicochemical properties and soil fungal and bacterial community composition, and a partial least squares path model (PLS-PM) was constructed to express the causal relationship between soil physicochemical properties and soil bacterial and fungal community diversity. The results showed that the soil bacterial species richness was highest in vegetable land and the lowest in the wasteland. Proteobacteria is the dominant phylum (20.69%–32.70%), and Actinobacteria is the dominant class (7.99%–16.95%). The species richness of fungi in woodland was the highest, while was the lowest in cultivated land. The dominant phylum of fungi in vegetable land, woodland, and cultivated land is Mucoromycota, 29.39%, 41.36%, and 22.67%, respectively. Ascomycota (42.16%) is the dominant phylum in wasteland. Sordariomyetes of Ascomycota is the dominant class in wasteland and cultivated land. Mortierellomycetes and Glomeromycetes of Mucoromycota are the dominant class in vegetable land and woodland. The results of the Spearman analysis revealed that the dominant groups in the bacterial and fungal communities had significant correlations with soil pH, clay, and sand (p &lt; 0.01). The RDA results showed that soil clay, pH, and moisture were the key environmental factors affecting the diversity of soil microbial communities. Fungal diversity is more affected by different land use patterns than bacteria. These results provided a theoretical basis for the changes in soil microbial community composition and diversity in river basins.

Microbial decomposition processes are typically described using first‐order kinetics, and the effect of elevated temperature is modeled as an increase in the rate constant. However, there is experimental data to suggest that temperature increases the pool size of substrate C available for microbial respiration with little effect on first‐order rate constants. We reasoned that changes in soil temperature alter the composition of microbial communities, wherein dominant populations at higher temperatures have the ability to metabolize substrates that are not used by members of the microbial community at lower temperatures. To gain insight into changes in microbial community composition and function following soil warming, we used molecular techniques of phospholipid fatty acid (PLFA) and lipopolysaccharide fatty acid (LPS‐OHFA) analysis and compared the kinetics of microbial respiration for soils incubated from 5 to 25°C. Substrate pools for microbial respiration and the abundance of PLFA and LPS‐OHFA biomarkers for Gram‐positive and Gram‐negative bacteria differed significantly among temperature treatments, providing evidence for a shift in the function and composition of microbial communities related to soil warming. We suggest that shifts in microbial community composition following either large seasonal variation in soil temperature or smaller annual increases associated with global climate change have the potential to alter patterns of soil organic matter decomposition by a mechanism that is not considered by current simulation models.

EDITORIAL article Front. Microbiol., 26 September 2014Sec. Terrestrial Microbiology Volume 5 - 2014 | https://doi.org/10.3389/fmicb.2014.00497