Dominant Bacterial Taxa Research Articles

Community composition and co-occurrence of free-living and particle-attached bacteria in the source region of the Ganges and Brahmaputra Rivers.

Bacteria have two trophic lifestyles in aquatic ecosystems, i.e., free-living (FL) and particle-attached (PA), with different but essential ecological roles. However, relevant knowledge is still dearth in the upstream source region of the Himalayan Rivers. Thus, we emphasized a comparative study on community composition, co-occurrence, and geographic distribution of the FL and PA bacteria and the effect of environmental factors in the source region of the Ganges and Brahmaputra Rivers. PA bacteria relative to FL harbored a significantly higher local diversity, richness, and evenness. A significantly higher abundance of Betaproteobacteria, Verrucomicrobiota, and Planctomycetota in PA trophic lifestyle and Gammaproteobacteria and Actinomycetota in FL tropic lifestyle and indicator OTUs belonging to related taxa were observed. The spatial variation of the FL and PA bacterial communities was most significantly impacted by dispersal limitation as a discrete factor. Among the environmental parameters, the total nitrogen (TN) was found to be a significant (P < 0.001) driver of the variation in PA communities. Meanwhile, particulate organic carbon (POC) and TN considerably explained the variation of FL communities. A significant correlation (P < 0.001) of TN with dominant bacterial taxa (Pseudomonadota, Actinomycetota, and Verrucomicrobiota) and FL and PA indicator OTUs associated with these taxa further confirmed nitrogen as the limiting nutrient in the source region of the Ganges and Brahmaputra Rivers. The co-occurrence network topological characteristics showed that the PA network was more stable than the FL network, which was more complicated and unstable. Thus, it can be speculated that FL communities relative to PA are more vulnerable to shifting upon disturbances.

The gut microbiota of healthy individuals remains resilient in response to the consumption of various dietary fibers

This study focuses on the resilience of gut microbiota during a five-month multi-interventional nutrition trial. The modulatory effects of beta-glucan, rye bran and two dietary fiber mixtures on the fecal pH and compositional changes of the microbiome of healthy subjects were studied. To analyze the stability of intestinal microbiota, we collected an extensive dataset of sequential fecal samples (23–29 from each participant) during a week of the base, beta-glucan consumption and wash-out periods accompanied by the collection of daily food diary data. Microbiota analyses were also conducted after the end of each fiber intake and wash-out period, along with measurements of fecal organic acids and pH. Based on the dominant bacterial taxa, two prevalent microbiota types were identified. The Prevotella-type microbiota responded more to the tested dietary fibers, while the Bacteroides-type microbiota was the least affected. Three microbiota types could not be clustered and behaved differently. Although we noted individual effects of definite fibers on participants’ gut microbiota and metabolic profile, relative abundances of bacteria remained stable in the base period (z-scores − 2.2 to 2.3). In most cases, the bacterial abundances of the final samples remained within the normal fluctuation range stressing out the resilience of healthy microbiota. The pH of all fecal samples varied between 6.1 and 8.3 and was associated with the concentration of organic acids and microbial composition. The effect of dietary fibers on the metabolism of fecal microbiota clearly depended on the individual microbiota type. Combining the analysis of gut microbiota with knowledge of the properties of dietary fibers would provide a powerful strategy for nutrition guidance and disease prevention.

Response of bacterial and fungal communities in natural biofilms to bioavailable heavy metals in a mining-affected river

Biofilms, known as “microbial skin” in rivers, respond to rapid and sensitive environmental changes. However, the ecological response mechanisms of bacterial and fungal communities in river biofilms toward heavy metal pollution (HMP) remains poorly understood. This study focused on the key driving factors of bacterial and fungal community diversity and composition and their ecological response mechanisms within periphytic biofilms of Asia's largest Pb–Zn mining area. The diversity, dominant bacterial taxa, and bacteria structure in biofilms were influenced by biologically available heavy metal (HM) fractions, with Ni-F3 (17.96 %) and Pb-F4 (16.27 %) as the main factors affecting the bacterial community structure. Fungal community structure and α-diversity were more susceptible to physicochemical parameters (pH and nutrient elements). Partial least squares path modeling revealed that environmental factors influencing bacterial and fungal communities in biofilms were ranked as water quality > metal fractions > total metals. Dispersal limitation was the most critical ecological process in bacterial (56.9 %) and fungal (73.4 %) assembly. The proportion of heterogeneous selection by bacteria (39.5 %) was higher than that of fungus (26.2 %), which increased with increasing HMP. Bacterial communities had a higher migration rate (0.48) and ecological drift proportion (3.6 %), making them more prone to escape environmental stress. Fungal communities exhibited more keystone species, larger niche width (23.24 ± 13.04 vs. 9.72 ± 5.48), higher organization level, and a more stable co-occurrence network than bacterial communities, which enabled them to better adapt to high environmental pollution levels. These findings expanded the understanding of the spatiotemporal dynamics of microbial communities within biofilms in HM-polluted watersheds and provided new insights into the ecological responses of microbial communities to HMP.

Characteristics of Rhizosphere Microbiome, Soil Chemical Properties, and Plant Biomass and Nutrients in Citrus reticulata cv. Shatangju Exposed to Increasing Soil Cu Levels.

The prolonged utilization of copper (Cu)-containing fungicides results in Cu accumulation and affects soil ecological health. Thus, a pot experiment was conducted using Citrus reticulata cv. Shatangju with five Cu levels (38, 108, 178, 318, and 388 mg kg-1) to evaluate the impacts of the soil microbial processes, chemistry properties, and citrus growth. These results revealed that, with the soil Cu levels increased, the soil total Cu (TCu), available Cu (ACu), organic matter (SOM), available potassium (AK), and pH increased while the soil available phosphorus (AP) and alkali-hydrolyzable nitrogen (AN) decreased. Moreover, the soil extracellular enzyme activities related to C and P metabolism decreased while the enzymes related to N metabolism increased, and the expression of soil genes involved in C, N, and P cycling was regulated. Moreover, it was observed that tolerant microorganisms (e.g., p_Proteobacteria, p_Actinobacteria, g_Lysobacter, g_Sphingobium, f_Aspergillaceae, and g_Penicillium) were enriched but sensitive taxa (p_Myxococcota) were suppressed in the citrus rhizosphere. The citrus biomass was mainly positively correlated with soil AN and AP; plant N and P were mainly positively correlated with soil AP, AN, and acid phosphatase (ACP); and plant K was mainly negatively related with soil β-glucosidase (βG) and positively related with the soil fungal Shannon index. The dominant bacterial taxa p_Actinobacteriota presented positively correlated with the plant biomass and plant N, P, and K and was negatively correlated with plant Cu. The dominant fungal taxa p_Ascomycota was positively related to plant Cu but negatively with the plant biomass and plant N, P, and K. Notably, arbuscular mycorrhizal fungi (p_Glomeromycota) were positively related with plant P below soil Cu 108 mg kg-1, and pathogenic fungi (p_Mortierellomycota) was negatively correlated with plant K above soil Cu 178 mg kg-1. These findings provided a new perspective on soil microbes and chemistry properties and the healthy development of the citrus industry at increasing soil Cu levels.

The Effect of Intercropping with Different Leguminous Green Manures on the Soil Environment and Tea Quality in Tea Plantations.

Intercropping with green manure is a soil-sustainable cultivation practice that has demonstrated positive impacts on tea growth and the soil environment in tea plantations. Nevertheless, research examining the effect of leguminous green manure varieties in tea plantations is scarce. This study aimed to analyze the tea quality and soil environment components in response to intercropping with three distinct leguminous green manures, Cassia sophera cv. Chafei 1 (CF), Sesbania cannabina (Retz.) Pers. (SC), and Chamaecrista rotundifolia (Pers.) Greene (CR), with 70% chemical fertilizer, and compare them to non-intercropped green manures with 100% chemical fertilizer (CK) in tea plantations. The findings indicated that intercropping with SC increased the amino acids content of tea leaves, the soil organic carbon (SOC), the soil acid phosphatase (ACP), the soil acid protease (ACPT), and the bacterial diversity compared to the CK treatment. Intercropping with CR improved the ACP activity and bacterial diversity while intercropping with CF improved the polyphenols. Proteobacteria, Acidobacteria, Actinomycetes, and Firmicutes were identified as the dominant bacterial taxa in tea plantations with intercropped green manure. A strong positive correlation was indicated between the SOC contents and the amino acids content in tea leaves after intercropping. A canonical correspondence analysis indicated significant associations between the ACP and the urease activity, and between the ACP and ACPT, and both were closely linked to SC. This finding provides an explanation that intercropping with SC may positively affect tea quality by influencing the SOC content, the soil enzyme activity, and the soil bacterial diversity. Green manure intercropping may replace part of chemical fertilizers, improve the soil environment in tea gardens, and enhance the quality of tea. These findings offer a theoretical reference for selecting leguminous green manure and advancing the sustainable development of tea plantations.

Comparative Analysis of Gut Bacterial Diversity in Wild and Domestic Yaks on the Qinghai-Tibetan Plateau.

The gut microbiota is a diverse and complex population, and it has a key role in the host's health and adaptability to the environment. The present study investigated the fecal bacterial community of wild grazing (WG) and domestic grazing (DG) yaks on natural grazing pastures, analyzing the gut microbiota using 16S rRNA sequencing to assess bacterial diversity. A total of 48 yak fecal samples were selected from two different grazing habitats. The DG group had more crude proteins and non-fiber carbohydrates. The WG group had more OM, insoluble dietary fiber such as NDF, ADF, ether extract, and TC. There were 165 and 142 unique operational taxonomic units (OTUs) in the WG and DG groups, respectively. Shannon index analysis revealed a higher bacterial diversity in the WG group than in the DG group. At the phylum level, Firmicutes were the dominant bacterial taxa in both groups. The relative abundance of Firmicutes in the WG group was higher than in the DG group. At the family level, the WG group had a significantly higher abundance of Ruminococcaceae (p < 0.001) and Rikenellaceae (p < 0.001) than the DG group. The abundances of Alloprevotella and Succinivibrio were more pronounced in the DG group than in the WG group at the genus level. This study presents a novel understanding of the bacterial communities of ruminants and their potential applications for livestock production.

Metabolites of blueberry roots at different developmental stages strongly shape microbial community structure and intra-kingdom interactions at the root-soil interface

The rhizosphere microorganisms of blueberry plants have long coexisted with their hosts under distinctively acidic soil conditions, exerting a profound influence on host performance through mutualistic symbiotic interactions. Meanwhile, plants can regulate rhizosphere microorganisms by exerting host effects to meet the functional requirements of plant growth and development. However, it remains unknown how the developmental stages of blueberry plants affect the structure, function, and interactions of the rhizosphere microbial communities. Here, we examined bacterial communities and root metabolites at three developmental stages (flower and leaf bud development stage, fruit growth and development stage, and fruit maturation stage) of blueberry plants. The results revealed that the Shannon and Chao 1 indices as well as community composition varied significantly across all three developmental stages. The relative abundance of Actinobacteria significantly increased by 10 % (p < 0.05) from stage 1 to stage 2, whereas that of Proteobacteria decreased significantly. The co-occurrence network analysis revealed a relatively complex network with 1179 edges and 365 nodes in the stage 2. Niche breadth was highest at stage 2, while niche overlap tended to increase as the plant developed. Furthermore, the untargeted metabolome analysis revealed that the number of differential metabolites of vitamins, nucleic acids, steroids, and lipids increased between stage 1 to stage2 and stage 2 to stage 3, while those for differential metabolites of carbohydrates and peptides decreased. Significant changes in expression levels of levan, L-glutamic acid, indoleacrylic acid, oleoside 11-methyl ester, threo-syringoylglycerol, gingerglycolipid B, and bovinic acid were highly correlated with the bacterial community structure. Collectively, our study reveals that significant alterations in dominant bacterial taxa are strongly correlated with the dynamics of root metabolites. These findings lay the groundwork for developing prebiotic products to enhance the beneficial effects of root microorganisms and boosting blueberry productivity via a sustainable approach.

Dominant Bacterial Taxa in Chernozems and Factors Affecting Their Abundance in the Bacterial Community

Dominant Bacterial Taxa in Chernozems and Factors Affecting Their Abundance in the Bacterial Community

Gut bacterial community of Cnaphalocrocis medinalis (Guenée) (Lepidoptera: Crambidae) is driven by rice varieties

AbstractTo understand the effect of diet on gut bacteria of Cnaphalocrocis medinalis (rice leaf folder, RLF), we compared the composition and diversity of gut bacterial community in C. medinalis larvae collected from three different rice variety fields of Minghui 82 (RLF1), Youngyong 15 (RLF2) and Minghui 2155 (RLF3), using culture‐independent PCR (V3 variable region)‐denaturing gradient gel electrophoresis (PCR‐DGGE) methods and hypervariable region (V4) of 16S rRNA sequenced by Illumina HiSeq platform. The DGGE result showed that the bacteria genera Asaia, Bacillus, Stenotrophomonas, Achromobacter and Serratia coexisted in the guts of RLF1, RLF2 and RLF3, while Cedecea, Burkholderia and Acinetobacter coexisted in the guts of RLF2 and RLF3. However, only the genus Enterococcus existed in the guts of RLF1, and Pantoea, Wolbachia and Tumebacillus in RLF3 larvae. A total of 25 bacterial phyla, 48 classes, 127 orders, 223 families, and 406 genera were identified when using 16s RNA sequencing, with 35 genera coexisted in RLF1, RLF2 and RLF3 larval guts, while 83, 36, 141 unique genera existed in RLF1, RLF2 and RLF3, respectively. The indices of ACE and Shannon were not significantly different among RLF1, RLF2 and RLF3. The dominant bacterial taxa were Proteobacteria, Bacteroidetes and Firmicutes at the phylum level, and Acinetobacter and Wolbachia at the genus level. The relative genus abundance for the genera with relative abundance (≥0.01) was significantly different among RLF1, RLF2 and RLF3. The findings indicated that different rice varieties had significant effects on the relative abundance of gut bacteria in RLF, which could provide new insights into the relationship between insect gut bacteria and their associated host plants.

Viral infection of an estuarine Synechococcus influences its co-occurring heterotrophic bacterial community in the culture.

Viruses are infectious and abundant in the marine environment. Viral lysis of host cells releases organic matter and nutrients that affect the surrounding microbial community. Synechococcus are important primary producers in the ocean and they are subject to frequent viral infection. In the laboratory, Synechococcus cultures are often associated with bacteria and such a co-existence relationship appears to be important to the growth and stability of Synechococcus. However, we know little about how viral lysis of Synechococcus affects the co-existing bacteria in the culture. This study investigated the influence of viral infection of Synechococcus on co-occurring bacterial community in the culture. We analyzed the community composition, diversity, predicted functions of the bacterial community, and its correlations with fluorescent dissolved organic matter (FDOM) components and nutrients after introducing a cyanophage to the Synechococcus culture. Cyanophage infection altered the bacterial community structure and increased the bacterial diversity and richness. Increased bacterial groups such as Bacteroidetes and Alphaproteobacteria and decreased bacterial groups such as Gammaproteobacteria were observed. Moreover, cyanophage infection reduced bacterial interactions but enhanced correlations between the dominant bacterial taxa and nutrients. Unique FDOM components were observed in the cyanophage-added culture. Fluorescence intensities of FDOM components varied across the cyanophage-infection process. Decreased nitrate and increased ammonium and phosphate in the cyanophage-added culture coupled with the viral progeny production and increased substance transport and metabolism potentials of the bacterial community. Furthermore, increased potentials in methane metabolism and aromatic compound degradation of the bacterial community were observed in the cyanophage-added culture, suggesting that cyanophage infections contribute to the production of methane-related compounds and refractory organic matter in a microcosm like environment. This study has the potential to deepen our understanding of the impact of viral lysis of cyanobacteria on microbial community in the surrounding water.

The gut microbiome of farmed Arctic char (Salvelinus alpinus) is shaped by feeding stage and nutrient presence.

The gut microbiome plays an important role in maintaining health and productivity of farmed fish. However, the functional role of most gut microorganisms remains unknown. Identifying the stable members of the gut microbiota and understanding their functional roles could aid in the selection of positive traits or act as a proxy for fish health in aquaculture. Here, we analyse the gut microbial community of farmed juvenile Arctic char (Salvelinus alpinus) and reconstruct the metabolic potential of its main symbionts. The gut microbiota of Arctic char undergoes a succession in community composition during the first weeks post-hatch, with a decrease in Shannon diversity and the establishment of three dominant bacterial taxa. The genome of the most abundant bacterium, a Mycoplasma sp., shows adaptation to rapid growth in the nutrient-rich gut environment. The second most abundant taxon, a Brevinema sp., has versatile metabolic potential, including genes involved in host mucin degradation and utilization. However, during periods of absent gut content, a Ruminococcaceae bacterium becomes dominant, possibly outgrowing all other bacteria through the production of secondary metabolites involved in quorum sensing and cross-inhibition while benefiting the host through short-chain fatty acid production. Whereas Mycoplasma is often present as a symbiont in farmed salmonids, we show that the Ruminococcaceae species is also detected in wild Arctic char, suggesting a close evolutionary relationship between the host and this symbiotic bacterium.

Grazing exclusion alters soil methane flux and methanotrophic and methanogenic communities in alpine meadows on the Qinghai-Tibet Plateau.

Grazing exclusion (GE) is an effective measure for restoring degraded grassland ecosystems. However, the effect of GE on methane (CH4) uptake and production remains unclear in dominant bacterial taxa, main metabolic pathways, and drivers of these pathways. This study aimed to determine CH4 flux in alpine meadow soil using the chamber method. The in situ composition of soil aerobic CH4-oxidizing bacteria (MOB) and CH4-producing archaea (MPA) as well as the relative abundance of their functional genes were analyzed in grazed and nongrazed (6 years) alpine meadows using metagenomic methods. The results revealed that CH4 fluxes in grazed and nongrazed plots were -34.10 and -22.82 μg‧m-2‧h-1, respectively. Overall, 23 and 10 species of Types I and II MOB were identified, respectively. Type II MOB comprised the dominant bacteria involved in CH4 uptake, with Methylocystis constituting the dominant taxa. With regard to MPA, 12 species were identified in grazed meadows and 3 in nongrazed meadows, with Methanobrevibacter constituting the dominant taxa. GE decreased the diversity of MPA but increased the relative abundance of dominated species Methanobrevibacter millerae from 1.47 to 4.69%. The proportions of type I MOB, type II MOB, and MPA that were considerably affected by vegetation and soil factors were 68.42, 21.05, and 10.53%, respectively. Furthermore, the structural equation models revealed that soil factors (available phosphorus, bulk density, and moisture) significantly affected CH4 flux more than vegetation factors (grass species number, grass aboveground biomass, grass root biomass, and litter biomass). CH4 flux was mainly regulated by serine and acetate pathways. The serine pathway was driven by soil factors (0.84, p < 0.001), whereas the acetate pathway was mainly driven by vegetation (-0.39, p < 0.05) and soil factors (0.25, p < 0.05). In conclusion, our findings revealed that alpine meadow soil is a CH4 sink. However, GE reduces the CH4 sink potential by altering vegetation structure and soil properties, especially soil physical properties.

Assessment of intestinal status in MPLW515L mutant myeloproliferative neoplasms mice model

The MPLW515L mutation is a prevalent genetic mutation in patients with myeloproliferative neoplasms (MPN), and utilizing this mutation in mice model can provide important insights into the disease. However, the relationship between intestinal homeostasis and MPN mice model remains elusive. In this study, we utilized a retroviral vector to transfect hematopoietic stem cells with the MPLW515L mutation, creating mutated MPN mice model to investigate their intestinal status. Our results revealed that the MPLW515L in MPN mice model aggravated inflammation in the intestines, decreased the levels of tight junction proteins and receptors for bacteria metabolites. Additionally, there was increased activation of the caspase1/IL-1β signaling pathway and a significant reduction in phos-p38 levels in the intestinal tissue in MPN mice. The MPLW515L mutation also led to up-expression of anti-microbial genes in the intestinal tract. Though the mutation had no impact on the alpha diversity and dominant bacterial taxa, it did influence the rare bacterial taxa/sub-communities and consequently impacted intestinal homeostasis. Our findings demonstrate the significance of MPLW515L mice model for studying MPN disease and highlight the mutation's influence on intestinal homeostasis, including inflammation, activation of the IL-1β signaling pathway, and the composition of gut microbial communities.

Fecal Metagenomics Study Reveals That a Low-Fiber Diet Drives the Migration of Wild Asian Elephants in Xishuangbanna, China.

The rare northward migration of wild Asian elephants in Xishuangbanna, China, has attracted global attention. Elephant migration is a complex ecological process, and the factors driving this long-distance migration remain elusive. In this study, fresh fecal samples were collected from both captive and wild Asian elephants, along with breastfed calves residing within the Wild Elephant Valley of Xishuangbanna. Our aim was to investigate the relationship between diet, gut microbiota, and migration patterns in Asian elephants through comprehensive metagenomic sequencing analyses. Among the breastfed Asian elephant group, Bacteroidales and Escherichia emerged as the dominant bacterial taxa, while the primary carbohydrate-active enzymes (CAZymes) enriched in this group were GH2, GH20, GH92, GH97, GH38, GH23, and GH43, aligning with their dietary source, namely breast milk. The bacterial taxa enriched in captive Asian elephants (CAEs) were mainly Butyrivibrio, Treponema, and Fibrobacter, and the enriched lignocellulose-degrading enzymes mainly included GH25, GH10, GH9, and cellulase (EC 3.2.1.4). These findings are consistent with the high-fiber diet of captive elephants. In contrast, the main bacterial taxa enriched in wild Asian elephants (WAEs) were Ruminococcus and Eubacterium, and the enriched CAZymes included GH109, GH20, GH33, GH28, GH106, and GH39. The abundance of lignocellulose-degrading bacteria and CAZyme content was low in WAEs, indicating challenges in processing high-fiber foods and explaining the low-fiber diet in this group. These findings suggest that wild elephant herds migrate in search of nutritionally suitable, low-fiber food sources.

Characterization of the bacterial microbiota of cattle ticks in northeastern Thailand through 16S rRNA amplicon sequencing

Ticks are vectors of a variety of pathogens that can infect humans and animals. Ticks also harbor non-pathogenic microbiota. This study characterized the microbiota of the ticks infesting beef cattle in Thailand. Two species of ticks; Rhipicephalus microplus (n = 15) and Haemaphysalis bispinosa (n = 5), were collected in seven provinces in northeastern Thailand. Microbial community profile of ticks was examined based on sequences of the V3-V4 region of 16S rRNA gene. Proteobacteria (Pseudomonadota) was the most abundant phylum, followed by Firmicutes (Bacillota), and Actinobacteriota. Coxiella-like endosymbiont was the most abundant bacterial taxon overall (49% of sequence reads), followed by Anaplasma (8.5%), Corynebacterium (5.5%), Ehrlichia (3.9%), and Castellaniella (3.4%). Co-infections of the pathogenic bacteria Ehrlichia and Anaplasma were detected in 19/20 (95%) female ticks. The tick with the lowest number of bacteria had the lowest abundance of the Coxiella-like endosymbiont, and the pathogenic bacteria Anaplasma and Ehrlichia were absent. This study provides baseline information of the microbiota of cattle ticks in northeastern Thailand, suggesting that ticks carry a few dominant bacterial taxa that are primarily non-pathogenic but can co-occur with pathogenic microorganisms. The information obtained is useful for monitoring disease outbreaks in the future and informing prevention and control strategies against cattle tick-borne diseases.

Gut microbiota signature in children with autism spectrum disorder who suffered from chronic gastrointestinal symptoms

BackgroundChildren diagnosed with autism spectrum disorder (ASD) frequently suffer from persistent gastrointestinal symptoms, such as constipation and diarrhea. Various studies have highlighted differences in gut microbiota composition between individuals with ASD and healthy controls of similar ages. However, it’s essential to recognize that these disparities may be influenced by cultural practices, dietary habits, and environmental factors.MethodsIn this study, we collected fecal samples from both children diagnosed with ASD (n = 42) and healthy individuals (n = 41) residing in the southeastern coastal region of China. Subsequently, 16 S rRNA gene sequencing and advanced bioinformatics analyses were conducted to investigate the distinctive features of gut microbial communities within each group.ResultsThe ASD group consisted of 28 males and 14 females, with a median age of 5.8 years, while the control group included 25 males and 16 females, with a median age of 6.8 years. Among the 83 sequenced fecal samples, a total of 1031 operational taxonomic units (OTUs) were identified. These included 122 unique OTUs specific to the control group and 285 unique OTUs specific to the ASD group. Analyses of α-diversity and β-diversity unveiled significant differences in the abundance and composition of gut microbiota between the two groups. It was found that the dominant bacterial taxa in healthy individuals were UBA1819, Flavonifractor, and Bradyrhizobium. In contrast, the ASD group exhibited a prevalence of Streptococcus, Ruminococcus, and Ruminiclostridium. Further analysis using Kyoto Encyclopedia of Genes and Genomes (KEGG) and Clusters of Orthologous Groups (COG) showed significant differences in the metabolic functionalities of the gut microbiota between the two groups. Notably, the metabolic pathway related to alpha-linolenic acid (ALA) in the gut microbiota of the ASD group was notably diminished compared to the control group. Conversely, the ASD group demonstrated significantly elevated levels of metabolic pathways involving uncharacterized conserved proteins, aminoglycoside phosphotransferase, and inorganic pyrophosphatase compared to the control group.ConclusionsOverall, these results confirm that there are significant differences in the gut microbiota structure between children with ASD and healthy controls in the southeast coastal region of China. This underscores the critical significance of delving into clinical interventions capable of mitigating the gastrointestinal and psychological symptoms encountered by children with ASD. A particularly encouraging path for such interventions lies in the realm of fecal microbiota transplantation, a prospect that merits deeper inquiry.

Rhizosphere microbiomes of resurrection plants Ramonda serbica and R. nathaliae: comparative analysis and search for bacteria mitigating drought stress in wheat (Triticum aestivum L.).

Rhizosphere microbial communities play an important role in maintaining the health and productivity of the plant host. The rhizobacteria Pseudomonas putida P2 of Ramonda serbica and Bacillus cereus P5 of R. nathaliae were selected for treatment of the Belija wheat cultivar because of their plant growth-promoting (PGP) properties. Compared to the non-treated drought-stressed plants, the plants treated with rhizobacteria showed increased activity of the two major antioxidant enzymes, superoxide dismutase, and ascorbate peroxidase. Plants treated with the B. cereus P5 strain exhibited higher proline content under drought stress, suggesting that proline accumulation depends on the relative water content (RWC) status of the plants studied. Inoculation of wheat seeds with the P. putida P2 strain improved water status by increasing RWC and alleviating oxidative stress by reducing H2O2 and malondialdehyde concentrations in plants exposed to severe drought, possibly also helping plants to overcome drought through its 1-aminocyclopropane-1-carboxylic acid deaminase activity. Analysis of data from Next Generation sequencing (NGS) revealed that the dominant bacterial taxa in the rhizosphere of resurrection plants R. serbica and R. nathaliae were extremophilic, thermotolerant, Vicinamibacter silvestris, Chthoniobacter flavus, and Gaiella occulta. From the fungi detected Penicillium was the most abundant in both samples, while Fusarium and Mucor were present only in the rhizosphere of R. serbica and the entomopathogenic fungi Metarhizium, and Tolypocladiumu only in the rhizosphere of R. nathaliae. The fungal communities varied among plants, suggesting a stronger environmental influence than plant species. Our study demonstrates the importance of in vivo experiments to confirm the properties of PGP bacteria and indicates that the rhizosphere of resurrection plants is a valuable source of unique microorganisms that can be used to improve the drought stress tolerance of crops.

Relation analysis of bacterial community in soils of coal mines with potential ecological risk from heavy metals

Coal consumption increases consistently, and heavy metal contamination in soils surrounding coal mines has been a severe environmental issue. Investigation of the relations of the bacterial community in soils of coal mines with potential ecological risk from heavy metals is essential for better understanding the impact of coal production on ecosystem health. In this study, soils surrounding two coal mines in a typical coal industry city of China were sampled, and heavy metals (Cd, Cr, Ni, Cu, Zn, As, and Pb) were quantified together with an in-depth evaluation of bacterial community based on high-throughput sequencing. The individual and overall ecological risk from heavy metals were estimated, and their relations with the identified seven core bacteria were analyzed. For soils surrounding both coal mines, in phylum level, five dominant bacterial taxa (Proteobacteria, Acidobacteriota, Actinobacteria, Firmicutes, and Bacteroidota) were identified, and their differences in relative abundance were clearly revealed, even if the differences between the two mines were not significant. When evaluated in genus level, apparent differences in bacterial community structure and complexity were found. The soils with higher potential ecological risk showed relatively lower complexity for the bacterial community. Seven core bacteria were identified, and negative relations of their relative abundance with the individual and overall ecological risk from heavy metals were revealed. Two families (Halomonadaceae and Aeromonadaceae) and two genera (Oceanisphaera and Ignatzschineria) were found more sensitive to both the individual risk from arsenic and the overall risk from all heavy metals, suggesting their possibility as indicators of soil contamination by these metal elements. Different from these, Rhizobiaceae revealed a positive relation with the overall risk value, implying their strong tolerance to heavy metals and, therefore, possible effect in bioremediation and phytoremediation of heavy metal contaminated soils. These findings have great reference value for better understanding the impacts of heavy metal contamination induced by coal production.

Intercropping and nitrogen enhance eucalyptus productivity through the positive interaction between soil fertility factors and bacterial communities along with the maintenance of soil enzyme activities

AbstractThe nitrogen (N) demand of eucalyptus plantations is considered to be effectively supplemented by the addition of N‐fixing plants. However, the effects of intercropping combined with N fertilization on the enzyme activity, soil fertility, and bacterial relationships, such as bacterial‐mediated nutrient cycling, remain elusive. A pot experiment was performed to assess the effect of intercropping and fertilization on eucalyptus productivity, soil fertility, enzyme activity, and bacterial characteristics, in addition to any probable linkages between these factors and how the interactions promote eco‐friendly production in eucalyptus plantations. Intercropping eucalyptus combined with suitable N fertilization (3 g plant−1) resulted in a higher Chao1 and Shannon diversity of bacterial communities; increased soil fertility, pH, enzyme activity, and eucalyptus productivity; as well as generated a stronger positive interaction between dominant bacterial taxa and soil environmental variables. According to the network and structural equation model (SEM) analysis, the interaction between dominant bacterial taxa and soil environmental variables was clearly linked to N application, and deficient or excess N fertilizer may exert a detrimental effect on eucalyptus productivity. This suggests that reasonable N application in intercropping is a potentially sustainable solution for maintaining eucalyptus productivity and soil quality under N‐limited conditions.

Cloacal microbiota are biogeographically structured in larks from desert, tropical and temperate areas

BackgroundIn contrast with macroorganisms, that show well-documented biogeographical patterns in distribution associated with local adaptation of physiology, behavior and life history, strong biogeographical patterns have not been found for microorganisms, raising questions about what determines their biogeography. Thus far, large-scale biogeographical studies have focused on free-living microbes, paying little attention to host-associated microbes, which play essential roles in physiology, behavior and life history of their hosts. Investigating cloacal gut microbiota of closely-related, ecologically similar free-living songbird species (Alaudidae, larks) inhabiting desert, temperate and tropical regions, we explored influences of geographical location and host species on α-diversity, co-occurrence of amplicon sequence variants (ASVs) and genera, differentially abundant and dominant bacterial taxa, and community composition. We also investigated how geographical distance explained differences in gut microbial community composition among larks.ResultsGeographic location did not explain variation in richness and Shannon diversity of cloacal microbiota in larks. Out of 3798 ASVs and 799 bacterial genera identified, 17 ASVs (< 0.5%) and 43 genera (5%) were shared by larks from all locations. Desert larks held fewer unique ASVs (25%) than temperate zone (31%) and tropical larks (34%). Five out of 33 detected bacterial phyla dominated lark cloacal gut microbiomes. In tropical larks three bacterial classes were overrepresented. Highlighting the distinctiveness of desert lark microbiota, the relative abundances of 52 ASVs differed among locations, which classified within three dominant and 11 low-abundance phyla. Clear and significant phylogenetic clustering in cloacal microbiota community composition (unweighted UniFrac) showed segregation with geography and host species, where microbiota of desert larks were distinct from those of tropical and temperate regions. Geographic distance was nonlinearly associated with pairwise unweighted UniFrac distances.ConclusionsWe conclude that host-associated microbiota are geographically structured in a group of widespread but closely-related bird species, following large-scale macro-ecological patterns and contrasting with previous findings for free-living microbes. Future work should further explore if and to what extent geographic variation in host-associated microbiota can be explained as result of co-evolution between gut microbes and host adaptive traits, and if and how acquisition from the environmental pool of bacteria contributes to explaining host-associated communities.