Microbial Community Composition Research Articles

Increasing tree phylogenetic diversity stimulates microbial functional potential in a subtropical forest

Abstract Soil microbial functions are closely related to ecosystem productivity, carbon sequestration and their responses to global change. Tree phylogenetic diversity has been found to impact microbial community composition, diversity, and functions, but how it modulates the linkage between microbial community facets and functions remains unclear. Here, 45 plots covering a natural gradient of tree phylogenetic diversity (TPD) were selected in a subtropical forest of southwest China to explore how increasing TPD impacts soil microbial community facets and microbial functional potential. The microbial functional potential was evaluated based on the abundances of carbon, nitrogen, and phosphorus cycling-related functional genes. Soil fungal alpha diversity increased significantly, but bacterial alpha diversity did not change as TPD increased. Both soil microbial network complexity and stability improved significantly with increasing TPD. Ultimately, increasing TPD promoted soil microbial functional potential by stimulating soil carbon and nitrogen availability, microbial keystone diversity, and network stability collectively. These findings emphasize the critical roles of keystone taxa and network stability as microbial factors in stimulating soil microbial function in response to increasing TPD. Therefore, it is strongly recommended to increase TPD in order to stimulate soil microbial functions and other ecosystem functions when implementing afforestation or ecological restoration projects.

Multi-omics analysis of soil microbiota and metabolites in dryland wheat fields under different tillage methods

No-tillage and subsoiling can improve soil aggregate structure and realize a synergistic effect of soil carbon and nitrogen retention compared with deep tillage. This study aimed to investigate the effects of different tillage methods on the microbiome and metabolites in wheat rhizosphere. Results indicated that no significant differences in the diversity of soil bacterial and fungal communities were observed among the tillage methods. Analysis revealed that no-tillage enriched specific genera such as Cryptosporangium, Crossiella, Rhodothermaceae, Leptothrix, Stilbella, Diutina, and Pyrenochaetopsis, while subsoiling was associated with Rubrobacter, Latescibacteraceae, Nitrospira, Rokubacteriales, and Ctenomyces. Deep tillage, on the other hand, showed significant associations with Nocardia, Aeromicrobium, Sphingopyxis, Cordyceps, and Subulicystidium. Metabolomic analysis identified differential metabolites involved in various pathways, including the biosynthesis of plant secondary metabolites, ABC transporters, and starch and sucrose metabolism. Correlation analysis revealed a significant interaction between microorganisms and metabolites in wheat rhizosphere. Bacteria at the genus level exhibited greater associations with differential metabolites. In conclusion, different tillage practices can alter the composition of microbial communities and metabolites in wheat rhizosphere, and their interactions may affect soil fertility and wheat growth.

Effects of parental care on skin microbial community composition in poison frogs.

Parent-offspring interactions constitute the first contact of many newborns with their environment, priming community assembly of microbes through priority effects. Early exposure to microbes can have lasting influences on the assembly and functionality of the host's microbiota, leaving a life-long imprint on host health and disease. Studies of the role played by parental care in microbial acquisition have primarily focused on humans and hosts with agricultural relevance. Anuran vertebrates offer the opportunity to examine microbial community composition across life stages as a function of parental investment. In this study, we investigate vertical transmission of microbiota during parental care in a poison frog (Family Dendrobatidae), where fathers transport their offspring piggyback-style from terrestrial clutches to aquatic nurseries. We found that substantial bacterial colonization of the embryo begins after hatching from the vitelline envelope, emphasizing its potential role as microbial barrier during early development. Using a laboratory cross-foster experiment, we demonstrated that poison frogs performing tadpole transport serve as a source of skin microbes for tadpoles on their back. To study how transport impacts the microbial skin communities of tadpoles in an ecologically relevant setting, we sampled frogs and tadpoles of sympatric species that do or do not exhibit tadpole transport in their natural habitat. We found more diverse microbial communities associated with tadpoles of transporting species compared to a non-transporting frog. However, we detected no difference in the degree of similarity between adult and tadpole skin microbiotas, based on whether the frog species exhibits transporting behavior or not. Using a field experiment, we confirmed that tadpole transport can result in the persistent colonization of tadpoles by isolated microbial taxa associated with the caregiver's skin, albeit often at low prevalence. This is the first study to describe vertical transmission of skin microbes in anuran amphibians, showing that offspring transport may serve as a mechanism for transmission of parental skin microbes. Overall, these findings provide a foundation for further research on how vertical transmission in this order impacts host-associated microbiota and physiology.

Perennial crops shape the soil microbial community and increase the soil carbon in the upper soil layer

Soil biodiversity is threatened by intensive agriculture that relies on annual grain crop production, thus leading to a decline in soil functions and ecosystem services. Perennial grain crops have a positive impact on the soil microbial community, but the responsive microbial groups and the magnitude of their response remain uncertain. To elucidate this, we analysed soil microbial biomass and community composition, bacterial growth and soil total carbon in five crops: organic perennial intermediate wheatgrass (IWG, Thinopyrum intermedium, Kernza®), organic IWG-alfalfa intercrop, organic biennial grass-legume mixture, organic annual wheat or rye and conventional annual wheat. The analysis was carried out at three time points under two growing seasons at four different soil depths. Five years after establishment, IWG had greater amounts of soil total fungi and bacteria, and of arbuscular mycorrhizal (AM) fungi, saprotrophic fungi, gram-negative (G−) and gram-positive (G+) bacteria compared to annual wheat. Crop perenniality influenced the soil microbial community structure although precipitation, soil temperature and water content were the main drivers of the patterns of and temporal variations in the microbial community. Perennial crops, with reduced tillage and low nitrogen input management increased the proportions of fungi relative to bacteria, AM fungi to saprotrophic fungi, G− bacteria to G+ bacteria, and the growth rate of total bacteria. This resulted in a more active soil microbial community with higher microbial biomass than annual wheat and contributed to the increased soil total carbon storage in the 0–5 cm soil layer in a humid continental climate. The findings emphasize the importance of combining a no tillage strategy with long-term vegetation cover to increase soil quality.

Machine Learning Reveals Microbial Taxa Associated with a Swim across the Pacific Ocean.

Purpose: This study aimed to characterize the association between microbial dynamics and excessive exercise. Methods: Swabbed fecal samples, body composition (percent body fat), and swimming logs were collected (n = 94) from a single individual over 107 days as he swam across the Pacific Ocean. The V4 region of the 16S rRNA gene was sequenced, generating 6.2 million amplicon sequence variants. Multivariate analysis was used to analyze the microbial community structure, and machine learning (random forest) was used to model the microbial dynamics over time using R statistical programming. Results: Our findings show a significant reduction in percent fat mass (Pearson; p < 0.01, R = -0.89) and daily swim distance (Spearman; p < 0.01, R = -0.30). Furthermore, the microbial community structure became increasingly similar over time (PERMANOVA; p < 0.01, R = -0.27). Decision-based modeling (random forest) revealed the genera Alistipes, Anaerostipes, Bifidobacterium, Butyricimonas, Lachnospira, Lachnobacterium, and Ruminococcus as important microbial biomarkers of excessive exercise for explaining variations observed throughout the swim (OOB; R = 0.893). Conclusions: We show that microbial community structure and composition accurately classify outcomes of excessive exercise in relation to body composition, blood pressure, and daily swim distance. More importantly, microbial dynamics reveal the microbial taxa significantly associated with increased exercise volume, highlighting specific microbes responsive to excessive swimming.

Metagenomic Analysis: Alterations of Soil Microbial Community and Function due to the Disturbance of Collecting Cordyceps sinensis

Soil microorganisms are critical to the occurrence of Cordyceps sinensis (Chinese Cordyceps), a medicinal fungi used in Traditional Chinese Medicine. The over-collection of Chinese Cordyceps has caused vegetation degradation and impacted the sustainable occurrence of Cordyceps. The effects of Chinese Cordyceps collection on soil microorganisms have not been reported. Metagenomic analysis was performed on the soil of collecting and non-collecting areas of production and non-production areas, respectively. C. sinensis collection showed no alteration in alpha-diversity but significantly affected beta-diversity and the community composition of soil microorganisms. In Cordyceps production, Thaumarchaeota and Crenarchaeota were identified as the dominant archaeal phyla. DNA repair, flagellar assembly, propionate metabolism, and sulfur metabolism were affected in archaea, reducing the tolerance of archaea in extreme habitats. Proteobacteria, Actinobacteria, Acidobacteria, Verrucomicrobia, and Nitrospirae were identified as the dominant bacterial phyla. The collection of Chinese Cordyceps enhanced the bacterial biosynthesis of secondary metabolites and suppressed ribosome and carbon metabolism pathways in bacteria. A more complex microbial community relationship network in the Chinese Cordyceps production area was found. The changes in the microbial community structure were closely related to C, N, P and enzyme activities. This study clarified soil microbial community composition and function in the Cordyceps production area and established that collection clearly affects the microbial community function by altering microbial community structure. Therefore, it would be important to balance the relationship between cordyceps production and microbiology.

Revealing the Response of Cucumber Soil Microbial Community Composition and Function to Nitrogen Addition in Northern Chinese Greenhouses

At present, the soil of Chinese greenhouses is experiencing severe nitrogen input in the form of fertilizer, which will cause damage to the soil environment and restrict crop growth in the long run. The response of potential functions of microorganisms as drivers of nutrient cycling and material transformation to nitrogen enrichment has rarely been reported in northern vegetable planting systems. Therefore, we set up four cucumber pot experiments with different nitrogen addition rates (0, 258, 516, and 1032 kg N ha−1 yr−1) in the greenhouse. Bacterial and fungal communities were detected by 16S and ITS rRNA gene sequencing, and bacterial and fungal functional groups were predicted using the FAPROTAX and FUNGuild databases. The findings showed that nitrogen addition induced soil acidification (a decrease of 0.25–1.63 units) significantly reduced microbial diversity and changed the community composition of bacteria and fungi. The relative abundance of bacterial functional groups associated with the nitrogen cycle increased significantly when medium and high levels of nitrogen were added. Conversely, the bacterial functional groups involved in the carbon cycle exhibited the opposite pattern. In this study, NO3− and soil pH were the main factors affecting the soil microbial community and its functional groups. Our results highlight that hydrocarbon degradation and saprophytic fungi may play key roles in yield formation during cucumber cultivation in northern solar greenhouses. In general, adopting a fertilization strategy that ensures low-medium nitrogen availability can contribute to the sustainable progress of facility agriculture.

Rice husk biochar is more effective in blocking the cadmium and lead accumulation in two Brassica vegetables grown on a contaminated field than sugarcane bagasse biochar.

Heavy metal-contaminated soil has a great impact on yield reduction of vegetable crops and soil microbial community destruction. Biochar-derived waste biomass is one of the most commonly applied soil conditioners in heavy metal-contaminated soil. Different heavy metal-contaminated soil added with suitable biochars represent an intriguing way of the safe production of crops. This study investigated the effects of two types of biochar [rice husk biochar (RHB) and sugarcane bagasse biochar (SBB)] on Cd and Pb accumulation in Shanghaiqing (SHQ, a variety of Brassica campestris L.) and Fengyou 737 (FY, a variety of Brassica napus), as well as on the soil microbial community, through a field experiment. RHB and SBB were characterized by scanning electron microscopy, Fourier transform infrared spectroscopy, and Brunauer-Emmet-Teller method. The results showed that RHB and SBB displayed the higher pH, cation exchange capacity and pore properties, and the addition of RHB and SBB enhanced soil pH and rhizosphere microorganisms promoting vegetables yield. RHB treatments were more effective than SBB in reducing upward transfer of Cd and Pb, blocking the accumulation of Cd and Pb in the edible parts of SHQ and FY, and decreasing soil Cd and Pb bioavailability. Additionally, RHB and SBB changed the composition of the rhizosphere soil microbial community. The application of biochar promoted the growth of ecologically beneficial bacteria (Nitrospira, Opitutus, and Gemmatimonas) and fungi (Mortierella and Holtermanniella), whereas reducing the enrichment of plant pathogenic fungi (Alternaria, Stagonosporopsis, Lectera, and Periconia) in rhizosphere soil. Our findings demonstrated that the application of RHB significantly reduces Cd and Pb accumulation in the edible parts by decreasing the soil Cd and Pb bioavailability and altering the rhizosphere microbial community composition in two Brassica vegetables grown on Cd/Pb-contaminated soils. Thus, the application of two biochar, especially RHB is a feasible strategy for the safe production of vegetable crops in Cd/Pb co-contaminated soils.

Effects of dietary supplementation by modified palygorskite and essential oil/palygorskite complex on growth performance and intestinal flora composition of broilers with diarrhea

With the development trend of the industry, it can be seen that the substitution of antibiotics and reduction of zinc oxiden is still the hot spot of the industry. Diarrhea and inflammation occur frequently during livestock and poultry production, which is difficult to control. This experiment aimed to explore the effects and mechanisms of dietary supplementation of modified palygorskite (Mpal) and essential oil/ palygorskite composite (EO-PGS) on disease resistance and intestinal inflammatory damage in diarrhea broiler. In this experiment, there were a total of 420 broilers of 10-day-old selected and divided into 7 groups (n = 60), which were the nondiarrhea group fed with basal diet (normal control, NC), the diarrhea group fed with basal diet (diarrhea control, DC), and the rest were the diarrhea test group (diarrhea), supplemented with 1 kg/t, 2 kg/t and 4 kg/t of essential oils/ palygorskite complex (EO-PGS 1kg/T, EO-PGS 2kg/T, EO-PGS 4kg/T) in the basal diet, respectively, and 2 kg/t, 4 kg/t modified palygorskite group (Mpal 2kg/T, Mpal 4kg/T) in the basal diets, respectively. The experiment lasted for 8 d. The results showed that compared to normal broilers, the diarrhea index of diarrhea broilers remained around 2.0 with persistent mild diarrhea during the test period. The duodenal epithelial cells were damaged and shed, goblet cells increased, inflammatory cells infiltrated, diffuse congestion and hemorrhage in lamina propria, the serum lipopolysaccharides (LPS) content, and malondialdehyde (MDA) content increased significantly (P < 0.05). The serum superoxide dismutase (SOD) activity and immunoglobulin-M (IgM) levels significantly decreased, while serum immunoglobulin-G (IgG) and complement 3 (C3) levels significantly increased (P < 0.05). The expression of inflammatory cytokines interleukin-1β (IL-1β), interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α), and nuclear factor κB (NF-κB) in duodenal epithelial cells was significantly upregulated on d 5 (P < 0.05). The abundance of Bacteroides in the duodenum of diarrhea broilers was significantly decreased, while the abundance of Proteobacteria was significantly increased (P < 0.05). Feeding diets supplemented with EO-PSG and 4 kg/t Mpal increased the average weight of diarrhea broilers (P < 0.05), reduced diarrhea index, improved immunity by increasing serum IgG, IgM, C3 and complement 4 (C4) levels (P < 0.05), enhanced the activity of serum antioxidant enzyme glutathione peroxidase (GSH-PX) and SOD activity, reduced serum MDA content, serum LPS levels, and decreased the expression of proinflammatory factors in the duodenal epithelial cell on d 5 (P < 0.05), alleviated duodenal epithelial cell injury, hemorrhage, inflammation infiltration and intestinal injury of diarrhea broilers from d 5 to d 8. Meanwhile, supplemented with EO-PSG and Mpal in diets regulated the intestinal microbiota, significantly increased the abundance of Bacteroidetes and decreased the abundance of Proteobacteria at the phylum level (P < 0.05). Microbial richness and diversity of microbiota were significantly increased by feeding the diet supplemented with 2 kg/t EO-PGS. In the beta diversity of the intestinal flora of the diets supplemented with 4 kg/t Mpal and 2 kg/t EO-PGS, the microbial community composition could be relatively easily distinguished with NC and DC groups. As a result of LEfSe analysis, the diets supplemented with 2 kg/t EO-PGS f_Clostridiaceae and g_Coprococcus were enriched in the caecum of diarrhea broilers, and the diets supplemented with 4 kg/t Mpal o_Bacteroidales, f_Rikenllaceae and g_Peptococcus were enriched in caecum of diarrhea broilers, between normal and diarrhea broilers (P<0.05). In conclusion, dietary supplementation with EO-PGS and Mpal could improve disease resistance and alleviate intestinal inflammatory damage in diarrhea broilers, but the effect of 2 kg/t Mpal was not significant. It was recommended that 2 kg/t EO-PGS or 4 kg/t Mpal be added to the broilers' diet according to the degree of diarrhea, and continuous feeding for more than 5 d.

Coniferous Tree Species Identity and Leaf Aging Alter the Composition of Phyllosphere Communities Through Changes in Leaf Traits

Phyllosphere microorganisms are essential for plant growth and health. Although there are an increasing number of studies showing that the composition of phyllosphere communities varies among different plant species, it remains unclear whether and how their bacterial and fungal community composition predictably varies with plant traits and leaf age. In this study, we used high-throughput sequencing to explore the diversity and composition of phyllosphere communities in needles of different ages (originating from different cohorts) for three evergreen coniferous species (Pinus koraiensis, Picea koraiensis, and Abies nephrolepis). Our results indicated that Gammaproteobacteria (bacteria) and Dothideomycetes (fungi) were dominant in newly formed needles, whereas Actinobacteria (bacteria) and Eurotiomycetes (fungi) were dominant in perennial needles. Tree species identity and needle age were the main factors explaining the variations of the α diversity (species richness of phyllosphere communities) and β diversity (dissimilarity among phyllosphere communities). In particular, we found that leaf dry matter content, leaf mass per area, and total phosphorus content emerged as key predictors of composition and diversity of phyllosphere microbial communities, underscoring the major influence of tree species identity and needle age on phyllosphere communities through changes in plant functional traits. Finally, we found that the interaction between tree species identity and needle age also contributed significantly to explaining the diversity and composition of phyllosphere communities, probably because differences in plant functional traits or environmental conditions between new and perennial needles depend on tree growth rates and resource acquisition strategies. These findings provide new insights into the mechanisms of community assembly among different evergreen tree species and offer a better understanding of the interactions between plant traits and phyllosphere microorganisms during needle aging.

Evaluation of biocorrosion, biofouling, and health risks in the two study locations in danube alluvium

Within conducted research the results of microbiological investigations on specific metabolic (phenotypic) groups of bacteria that play crucial roles in the biogeochemical cycling of iron, manganese, nitrogen, sulfur, and carbon are presented. These bacteria are also involved in the development of biocorrosion and biofouling processes, with some posing risks to public health. Utilizing results from applied biological activity reaction tests (BART tests), processed using specialized software, potential risks for the development of microbiologically mediated corrosion, biofouling, and health risks were calculated for seven wells within two oxic sites in the Danube alluvium – Vinci and Veliko Gradište, Serbia. Moderate to high corrosion risk was determined for all seven wells at both sites (CR=5.4). Microbiological fouling risk was very high in three out of the seven investigated wells (PR=8.10). Among the seven sites studied, one site stood out based on the calculated high value of health risk coefficient (HR=8.10). The research results provide new insights into the microbiological role in aging wells in oxic groundwater of the Danube alluvium. It is demonstrated that the physicochemical composition and chemical species such as minerals, organic matter, and the specific composition of microbial communities in the studied groundwater have the potential to stimulate biocorrosion and the formation of deposits and biofilms within well structures. In addition to biochemical analyses, hydrogeological characteristics of the analyzed area are presented to define the geological stratigraphy, for which specific microbiological transformations would be expected based on the obtained results.

Intercropping of tobacco and maize at seedling stage promotes crop growth through manipulating rhizosphere microenvironment.

Changes in the rhizosphere microbiome and metabolites resulting from crop intercropping can significantly enhance crop growth. While there has been an increasing number of studies on various crop combinations, research on the intercropping of tobacco and maize at seedling stage remains limited. This study is the first to explore rhizosphere effects of intercropping between tobacco and maize seedling stages, we analyzed the nitrogen, phosphorus and potassium nutrients in the soil, and revealed the important effects on soil microbial community composition and metabolite profiles, thereby regulating crop growth and improving soil balance. Compared with mono-cropping, intercropping increased the biomass of the two crops and promoted the nutrient absorption of nitrogen, phosphorus and potassium. Under intercropping conditions, the activities of sucrase, catalase and nitrate reductase in tobacco rhizosphere soil and the content of available potassium, the activities of nitrate reductase and acid phosphatase in maize rhizosphere soil were significantly increasing. Rhizosphere soil bacterial and fungal communities such as Sphingomonas, Massilia, Humicola and Penicillium respond differently to crop planting patterns, and soil dominant microbial communities are regulated by environmental factors such as pH, Organic Matter, Available Potassium, Nitrate Reductase, and Urease Enzyme. Network analysis showed that soil microbial communities were more complex after intercropping, and the reciprocal relationship between bacteria and fungi was enhanced. The difference of metabolites in soil between intercropping and monocropping system was mainly concentrated in galactose metabolism, starch and sucrose metabolism pathway, and the content of carbohydrate metabolites was significantly higher than that of monocropping soil. Key metabolites such as D-Sucrose, D-Fructose-6-Phosphate, D-Glucose-1-Phosphatel significantly influence the composition of dominant microbial communities such as Sphingomonas and Penicillium. This study explained the effects of intercropping between flue-cured tobacco and maize on the content of soil metabolites and soil microbial composition in rhizosphere soil, and deepened the understanding that intercropping system can improve the growth of flue-cured crops seedlings through rhizosphere effects.

Tidal levels significantly change bacterial community composition in a tropical estuary during the dry season

AbstractEstuaries are usually characterized by strong spatial and temporal variability in water physicochemical conditions and are often largely affected by human activities. One important source of variability is caused by tides that can swiftly alter not only physicochemical conditions but also the abundance and composition of the biota. The effect of the diurnal tidal cycle on microbial community composition during different seasons remains uncertain, although this knowledge underlies having effective monitoring programs for water quality and potential identification of health risk conditions. In this study, we assessed the bacterioplankton community composition and diversity across four tidal water levels in a tropical estuary characterized by a mixed semidiurnal tide regime (i.e., two high and two low tides of varying amplitudes) during both dry and wet seasons. The bacterial community composition varied significantly among the four tidal levels, but only during the dry season, when the influence of the seawater intrusion was largest. Bacterial indicators’ taxa identified using the Indicator Value Index were found within Cyanobacteria, Actinobacteriota, Bacteroidota, and Proteobacteria. The indicator taxon Cyanobium sp. had a prominent presence across multiple tidal levels. The main predicted phenotypes of the bacterial communities were associated with potential pathogenicity, gram-negative, and biofilm formation traits. While there were no marked predicted phenotypic differences between seasons, pathogenic and gram-negative traits were more prevalent in the dry season, while biofilm formation traits dominated in the wet season. Overall, our findings underscore the intricate relationship between river hydrodynamics and bacterial composition variability and hint a significant human impact on the water quality of the Bangpakong River.

Regulating facility soil microbial community and reducing cadmium enrichment in lettuce by reductive soil disinfestation

The accumulation of cadmium (Cd) in facility soil is attracting increasing attention. Reductive soil disinfestation (RSD) is an effective soil disinfection method, while also having a certain passivating effect on Cd. The application of organic matter is crucial for the success of RSD, but the reduction efficiencies of different organic materials vary. Here, five treatments, namely untreated soil (CK), bean dregs (BD), peanut dregs (PD), sesame dregs (SD), and apple dregs (AD) were applied, and their performances in Cd immobilization in Cd-contaminated soil were assessed. Changes in soil properties and microbial communities were monitored. The results showed that the overall soil pH following RSD treatment decreased significantly, while organic matter, hydrolyzed nitrogen, available phosphorus, available potassium, exchangeable calcium, and exchangeable magnesium increased significantly. Compared to CK, the exchangeable (EX)-Cd contents after treatments SD and AD significantly decreased by 25.4% and 23.7%, respectively. RSD led to significant changes in the composition of soil microbial communities. SD treatment significantly increased the number of soil fungal operational taxonomic units (OTU), while BD, PD, and SD significantly increased the relative abundances of Bacteroidetes, Chloroflexi, Deinococus Thermus, and Basidiomycota in bacterial communities. The Gemmatimonadetes phylum showed a highly significant negative correlation with EX-Cd, indicating that it might have a positive effect on the fixation of Cd in polluted soil. SD significantly reduced the Cd content in the above-ground parts of lettuce by 74.76%, and had the least impact on lettuce biomass. It can be inferred that RSD is an ecologically effective method for the remediation of Cd pollution in facility soil by improving soil characteristics and altering microbial community composition to reduce Cd activity. However, further in-depth research is needed to optimize the types and amounts of organic materials applied.

Unveiling the Hidden Responses: Metagenomic Insights into Dwarf Bamboo (Fargesia denudata) Rhizosphere under Drought and Nitrogen Challenges.

Dwarf bamboo (Fargesia denudata) is a crucial food source for the giant pandas. With its shallow root system and rapid growth, dwarf bamboo is highly sensitive to drought stress and nitrogen deposition, both major concerns of global climate change affecting plant growth and rhizosphere environments. However, few reports address the response mechanisms of the dwarf bamboo rhizosphere environment to these two factors. Therefore, this study investigated the effects of drought stress and nitrogen deposition on the physicochemical properties and microbial community composition of the arrow bamboo rhizosphere soil, using metagenomic sequencing to analyze functional genes involved in carbon and nitrogen cycles. Both drought stress and nitrogen deposition significantly altered the soil nutrient content, but their combination had no significant impact on these indicators. Nitrogen deposition increased the relative abundance of the microbial functional gene nrfA, while decreasing the abundances of nirK, nosZ, norB, and nifH. Drought stress inhibited the functional genes of key microbial enzymes involved in starch and sucrose metabolism, but promoted those involved in galactose metabolism, inositol phosphate metabolism, and hemicellulose degradation. NO3--N showed the highest correlation with N-cycling functional genes (p < 0.01). Total C and total N had the greatest impact on the relative abundance of key enzyme functional genes involved in carbon degradation. This research provides theoretical and technical references for the sustainable management and conservation of dwarf bamboo forests in giant panda habitats under global climate change.

Conversion of broadleaf forest to plantation changes the assembly process and composition of soil microbial communities in a subtropical forest

Conversion of broadleaf forest to plantation changes the assembly process and composition of soil microbial communities in a subtropical forest

Bacillus subtilis Strain YJ-15, Isolated from the Rhizosphere of Wheat Grown under Saline Conditions, Increases Soil Fertility and Modifies Microbial Community Structure

Soil salinization during wheat cultivation considerably diminishes soil fertility and impedes wheat growth, primarily due to rhizosphere microbial community changes. Our study investigates the application of Bacillus subtilis YJ-15, a strain isolated from the rhizosphere of wheat cultivated in salinized soil, as a soil remediation agent. This strain has demonstrated significant salt tolerance, disease suppression capabilities, and growth-promoting attributes in previous studies. The wheat rhizosphere was examined to assess the impact of Bacillus subtilis YJ-15 on microbial community composition and soil fertility. Fertility of soil in saline soil was significantly increased by inoculating wheat with YJ-15. The microbial community structure within the wheat rhizosphere inoculated with Bacillus subtilis YJ-15 was analyzed through sequencing on the Illumina MiSeq platform. Phyla Proteobacteria and Acidobacteria were identified as the dominant bacteria. Basidiomycota, Mortierellomycota, and Ascomycota dominated the fungal phyla. Among the bacterial genera, Pseudomonas, Arthrobacter, and Bacillus were predominant. The predominant fungal genera included Alternaria, Cephalotrichum, Mortierella, and Chaetomium. A significant increase in Gaiella and Haliangium levels was observed in the YJ group compared to the control group. Additionally, the fungal genera Epicoccum, Sporidiobolus, and Lecythophora have significantly increased in YJ abundance. One of the potential benefits of Bacillus subtilis YJ-15 in the cultivation of wheat on salinized land is its ability to enhance the rhizosphere microbial community structure and improve soil fertility.

Microbial response to seasonal variation in arctic biocrusts with a focus on fungi and cyanobacteria

Biocrusts are crucial components of Arctic ecosystems, playing significant roles in carbon and nitrogen cycling, especially in regions where plant growth is limited. However, the microbial communities within Arctic biocrusts and their strategies for surviving the harsh conditions remain poorly understood. In this study, the microbial profiles of Arctic biocrusts across different seasons (summer, autumn, and winter) were investigated in order to elucidate their survival strategies in extreme conditions. Metagenomic and metatranscriptomic analyses revealed significant differences in microbial community composition among the sites located in different elevations. The bacterial communities were dominated by Actinobacteria and Proteobacteria, while the fungal communities were mainly represented by Ascomycota and Basidiomycota, with lichenized and saprotrophic traits prevailing. Cyanobacteria were primarily composed of heterocystous cyanobacteria. Furthermore, the study identified molecular mechanisms underlying cold adaptation, including the expression of heat shock proteins and cold-inducible RNA helicases in cyanobacteria and fungi. Overall, the microbial communities appear to be permanently well adapted to the extreme environment.

The simultaneous addition of chitosan and peat enhanced the removals of antibiotics resistance genes during biogas residues composting

Direct reuse of biogas residue (BR) has the potential to contribute to the dissemination of antibiotic resistance genes (ARGs). Although high-temperature composting has been demonstrated as an effective method for the harmless treatment of organic waste, there is few researches on the fate of ARGs in high-temperature composting of BR. This research examined the impact of adding 5% chitosan and 15% peat on physicochemical characteristics, microbial communities, and removal of ARGs during BR-straw composting in 12 Biolan 220L composters for 48 days. Our results showed that the simultaneous addition of chitosan and peat extended the high-temperature period, and increased the highest temperature to 74 °C and germination index. These effects could be attributed to the presence of thermophilic cellulose-decomposing genera (Thermomyces and Thermobifida). Although the microbial communities differed compositionally among temperature stages, their dissimilarity drastically reduced at final stage, indicating that the impact of different treatments on microbial community composition decreases at the end of composting. Peat had a greater impact on aerobic genera capable of cellulose degradation at thermophilic stage than chitosan. Surprisingly, despite the total copy number of ARGs significantly decreased during composting, especially in the treatment with both chitosan and peat, intl1 gene abundance significantly increased 2 logs at thermophilic stage and maintained high level in the final compost, suggesting there is still a potential risk of transmission and proliferation of ARGs. Our work shed some lights on the development of waste resource utilization and emerging contaminants removal technology.

Modulating phytoremediation: How drip irrigation system affect performance of active green wall and microbial community changes

A recent innovation in air phytoremediation is active green walls, which utilises biofiltration technology with airflow from mechanical ventilation. While this novel technology is gaining traction, the influence of irrigation on soil moisture, and subsequently the microbial communities that play a role in air filtration is untested. In this study, the application of drip irrigation techniques in active green walls were investigated for their influence on system performance. A modular green wall system was tested, with tests across 7 different plant species, as well as a substrate only control. Water distribution across the modules, the water-carrying capacity and airflow through the substrate were measured. The microbial community present, which is critical to the phytoremediation process, was quantified by identifying individual microbial phospholipid fatty acids (PLFA) within the substrate. Results demonstrated that the lower-speed drip irrigation reduced water consumption compared to the rapid system, and had generally more uniform moisture distribution. High flow drip irrigation resulted in a water pathway phenomenon, leading to uneven moisture distribution within the green wall, and this effect was accentuated with fibrous root plant species. Drip irrigation did not change microbial community composition across planted modules, apart from increasing fungi by 6%, but did wash out bacteria at the high flow rate used (−56.67%), thus low flow rate irrigation rate is more beneficial for both plant growth and microbial community composition. The current work provides evidence that drip irrigation has considerable effects on both substrate airflow rate and substrate microbial density: both key to system air cleaning performance.