Main Phyla Research Articles

Microplastics mediates the spread of antimicrobial resistance plasmids via modulating conjugal gene expression.

Antimicrobial resistance (AMR) and environmental degradation are existential global public health threats. Linking microplastics (MPs) and AMR is particularly concerning as MPs pollution would have significant ramifications on controlling of AMR; however, the effects of MPs on the spread and genetic mechanisms of AMR bacteria remain unclear. Herein, we performed Simonsen end-point conjugation to investigate the impact of four commonly used MPs on transfer of clinically relevant plasmids. The transfer breadth of a representative pA/C_MCR-8 plasmid across bacterial communities was confirmed by the cell sorting and 16S rRNA gene amplicon sequencing. Our study shows that exposure to four commonly found MPs promotes the conjugation rates of four clinically relevant AMR plasmids by up to 200-fold, when compared to the non-exposed group and that the transfer rates are MP concentrations demonstrate a positive correlation with higher transfer rates. Furthermore, we show that MPs induce the expression of plasmid-borne conjugal genes and SOS-linked genes such as recA, lexA, dinB and dinD. High-throughput sequencing of the broad transmission of plasmid pA/C_MCR-8, shows distribution over two main phyla, Pseudomonadota (50.0%-95.0%) and Bacillota (0.4%-2.0%). These findings definitively link two global health emergencies - AMR and environmental degradation via MPs, and to tackle global AMR, we must also now consider plastic utilisation and waste management.

The Effectiveness of an Anoxic-Oxic-Anoxic-Oxic Sequencing Batch Reactor System (A2/O2-SBR) to Treat Electroplating Wastewater and the Bacterial Community within the System

This study presents an examination of the effectiveness of an anoxic-oxic-anoxic-oxic sequencing batch reactor (A2/O2-SBR) for treating electroplating wastewater (EPWW). The A2/O2-SBR was monitored for 60 days and the bacterial composition in the treatment system was determined. The system consisted of four reactors, which had the following anoxic/oxic ratios: reactor-I, 0:9 h; reactor-II, 2:7 h; reactor-III, 4.5:4.5 h; and reactor-IV, 7:2 h. The combined cycle time of the reactors was 12 h, the hydraulic retention time (HRT) was five days, and the total volume of mixed liquor suspended solids (MLSS) was 2,000 mg/L. The results demonstrate the importance of an anoxic period for the treatment of heavy metals. Most of the ammonium nitrogen (NH4+-N), Total Kjeldahl nitrogen (TKN), and total nitrogen (TN) were removed during the oxic period. However, as the anoxic period increased, the amounts of TKN, nitrite nitrogen (NO2--N), nitrate nitrogen (NO3--N), and TN declined. Reactor-IV showed a high removal efficiency for heavy metals (Zn2+, 89.74%; Cd2+, 81.37%), TKN (89.20%), and TN (84.25%), and also effectively treated NH4+-N (78.84%), biochemical oxygen demand (BOD5; 93.5%), and chemical oxygen demand (COD; 84.9%). Reactor-IV showed an appropriate difference in the dissolved oxygen (DO) concentration between the anoxic period and oxic period (2.12-2.00 mg/L). The main bacterial phyla in the treatment system were Proteobacteria, Actinobacteria, and Firmicutes, while Pseudomonas vancouverensis and Cryobacterium arcticum were the most common species. The anoxic period and bacterial community have significantly demonstrated the ability to remove Zn2+ and Cd2+ for effective treatment of EPWW.

Effects of High-Concentrate Diets on Growth Performance, Serum Biochemical Indexes, and Rumen Microbiota in House-Fed Yaks.

The aim of this study is to determine the effects of a high-concentrate diet on growth performance, serum biochemical indexes, and rumen microbiota in house-fed yaks. Sixteen male yaks (body weight, 151.73 ± 14.11 kg; 18 months) were randomly allocated into two dietary treatments: a group with a low level of concentrate (n = 8, LC, concentrate-forage = 40:60) and a group with a high level of concentrate (n = 8, HC, concentrate-forage = 60:40). We found that compared with the LC group, the average daily feed intake (ADFI), the average daily gain (ADG), and the serum albumin (ALB) concentration in the HC group were significantly increased (p < 0.05). The rumen bacterial compositions also differed significantly between the groups, as indicated by principal coordinate analysis (p < 0.05). Firmicutes and Bacteroidota were the main dominant phyla of rumen bacteria in yaks. Compared with the LC group, the relative abundance of Firmicutes in the HC group was significantly increased (p < 0.05) and the relative abundance of Bacteroidota was significantly decreased (p < 0.05). At the genus level, Rikenellaceae_RC9_gut_group, Succiniclasticum, Prevotella, Christensenellaceae_R-7_group, and NK4A214_group had the highest relative abundance. The relative abundance of Christensenellaceae_R-7_group in the HC group was significantly higher than that in the LC group (p < 0.05). The PICRUSt 2 results showed a significant enrichment in glycosaminoglycan degradation, apoptosis, and ECM-receptor interaction in HC relative to LC (p < 0.05). In conclusion, high-concentrate diets can enhance growth performance and alter the compositions and functions of ruminal bacterial communities in yaks.

Phylogenetic Analysis of 590 Species Reveals Distinct Evolutionary Patterns of Intron-Exon Gene Structures Across Eukaryotic Lineages.

Introns are highly prevalent in most eukaryotic genomes. Despite the accumulating evidence for benefits conferred by the possession of introns, their specific roles and functions, as well as the processes shaping their evolution, are still only partially understood. Here, we explore the evolution of the eukaryotic intron-exon gene structure by focusing on several key features such as the intron length, the number of introns, and the intron-to-exon length ratio in protein-coding genes. We utilize whole-genome data from 590 species covering the main eukaryotic taxonomic groups and analyze them within a statistical phylogenetic framework. We found that the basic gene structure differs markedly among the main eukaryotic groups, with animals, and particularly chordates, displaying intron-rich genes, compared with plants and fungi. Reconstruction of gene structure evolution suggests that these differences evolved prior to the divergence of the main phyla and have remained mostly conserved within groups. We revisit the previously reported association between the genome size and the mean intron length and report that this association differs considerably among phyla. Analyzing a large and diverse dataset of species with whole-genome information while applying advanced modeling techniques allowed us to obtain a global evolutionary perspective. Our findings may indicate that introns play different molecular and evolutionary roles in different organisms.

Mercury and Arctic Char Gill Microbiota Correlation in Canadian Arctic Communities.

Arctic char is a top predator in Arctic waters and is threatened by mercury pollution in the context of changing climate. Gill microbiota is directly exposed to environmental xenobiotics and play a central role in immunity and fitness. Surprisingly, there is a lack of literature studying the effect of mercury on gill microbiota. To fill this knowledge gap, our primary goal was to measure to what extent gill exposure to mercury may alter gill microbiota activity in Arctic char. Specifically, we calculated the correlation between the taxonomic distribution of gill-associated bacterial symbiont activity and total mercury concentration in livers and muscles in wild populations of Arctic char in the Canadian Arctic. Our results showed that total mercury concentrations in tissues were higher in Ekaluktutiak (Nunavut) than in the other sites in Nunavik. Proteobacteria was the main phylum correlated to mercury concentration in both tissues, followed by Bacteroidetes and Cyanobacteria. In the most contaminated sites, Aeromonas and Pseudomonas (Proteobacteria) were predominant, while mercury concentration negatively correlated with Photobacterium (Proteobacteria) or Cerasicoccus (Verrucomicrobia). In summary, we found that mercury contamination correlates with active gill microbiota composition, with potential implications of strains in modulating mercury toxicity, making them interesting for future biomarker studies.

Drip irrigation affects soil bacteria primarily through available nitrogen and soil fungi mainly via available nutrients.

The issue of water scarcity is a global concern. Water-saving irrigation has long been a topic of interest among agricultural researchers. In this study, changes in soil microbial community structure and diversity under different periods of drip irrigation were analyzed using the Illumina HiSeq high-throughput sequencing platform and 16S rRNA gene sequence amplification. Six treatments were established based on varying drip irrigation amounts: maintaining the drip irrigation amount at 320 mm without any increase (CK), increasing by 72 mm during different growth stages: from the sowing stage to the jointing stage (J), from the jointing stage to the big trumpet stage (B), from the big trumpet stage to the tasseling stage (T), from the tasseling stage to the grain filling stage (G), and from the grain filling stage to the maturity stage (M). Compared to CK, the T treatment significantly increased the Chao index of soil bacteria by 2.95%. The main bacterial phyla included Proteobacteria, Acidobacteria, blastomonas, Actinobacteria, Chloromycetes, and Bacteroidetes, while ascomycetes, basidiomycetes, chytridomycetes, and mortieromycetes were the main fungal phyla across different periods of drip irrigation. Zoopagales, Amtridomyces, and Trichomyces were absent in the G, T, and M treatments, respectively. The content of soil-available potassium in the T treatment was higher than that in other treatments, whereas the content of soil-available nutrients in the B treatment was the lowest. Overall, the T treatment had the highest content of available nutrients. Redundancy analysis showed that available nitrogen was the main soil chemical property affecting soil bacterial community structure, while soil-available nutrients were the main soil chemical property affecting the fungal community structure. Thus, the T treatment was effective in enhancing soil microbial community structure and increasing soil-available nutrients.

Investigating the evolution of green algae with a large transcriptomic data set.

The colonization of land by plants approximately 450-500 million years ago (Mya) is one of the most important events in the history of life on Earth. Land plants, hereafter referred to as "embryophytes," comprise the foundation of every terrestrial biome, making them an essential lineage for the origin and maintenance of biodiversity. The embryophytes form a monophyletic clade within one of the two major phyla of the green algae (Viridiplantae), the Streptophyta. Estimates from fossil data and molecular clock analyses suggest the Streptophyte algae (Charophytes) diverged from the other main phylum of green algae, the Chlorophyta, as much as 1500 Mya. Here we present a phylogenetic analysis using transcriptomic and genomic data of 62 green algae and embryophyte operational taxonomic units, 31 of which were assembled de novo for this project. We have focused on identifying the charophyte lineage that is sister to embryophytes, and show that the Zygnematophyceae have the strongest support, followed by the Charophyceae. Furthermore, we have examined amino acid and codon usage across the tree and determined these data broadly follow the phylogenetic tree. We concluded by searching the data set for protein domains and gene families known to be important in embryophytes. Many of these domains and genes have homologous sequences in the charophyte lineages, giving insight into the processes that underlay the colonization of the land by plants. This provides new insights into green algal diversification, identifies previously unknown attributes of genome evolution within the group, and shows how functional mechanisms have evolved over time.

Study on Phosphorus Variability Characteristics and Response Mechanism of Microbial Community during Sediment Resuspension Process

Submerged plants and related disturbances can affect both the phosphorus (P) release and the microbial communities in sediments. In this study, a sediment resuspension system was constructed, and P variability characteristics influenced by Vallisneria natans (V. natans) and the response mechanism of the microbial community were studied. The results indicated that the total phosphorus (TP) content increased from 678.875 to 1019.133 mg/kg and from 1126.017 to 1280.679 mg/kg in sediments and suspended solids (SSs) during the sediment resuspension process, respectively. Organic P (OP) increased by 127.344 mg/kg and 302.448 mg/kg in sediments and SSs after the disturbance, respectively. The microbial communities in the sediments and the leaves of V. natans had higher Chao values after the disturbance, while Shannon values decreased after the disturbance compared to the control in SSs. Proteobacteria had the highest abundance with the value of 51.1% after the disturbance in the sediments and SSs, and the abundance values of Proteobacteria in rhizomes and leaves of V. natans could reach 73.2% on average. Chloroflexi, Acidobacteria, and Firmicutes were also the main phyla in the sediment resuspension system. Sodium hydroxide extractable P (NaOH-P) in sediments could reduce the bioavailability of this P fraction under disturbance conditions. The decrease in the abundance of Bacteroidetes and Nitrospirae indicated that they were more sensitive to the disturbance, and the rotational speed changed the survival conditions for the Bacteroidetes and Nitrospirae. The response mechanism of microbial community during the sediment resuspension process could reflect the influence of the microbial community on the changing characteristics of P and could provide a theoretical foundation for P control at the micro level.

Comparative Analyses of Lycodon rufozonatus and Lycodon rosozonatus Gut Microbiota in Different Regions.

The interactions between hosts and the gut microbiota are intricate and can significantly affect the ecology and evolution of both parties. Various host traits, including taxonomy, diet, social behaviour, and external factors such as prey availability and the local environment, all play an important role in shaping composition and diversity of the gut microbiogta. In this study, we explored the impact of intestinal microorganisms on the host in adapting to their respective ecological niches in two species of snakes. We collected feces from Lycodon rufozonatus and Lycodon rosozonatus from different geographical locations and used 16S rRNA gene sequencing technology to sequence the v3-v4 region. The results revealed that there was no significant difference in the alpha diversity of intestinal microorganisms between L. rufozonatus and L. rosozonatus. The gut microbiota of all individuals comprised four main phyla: Pseudomonadota, Bacteroidota, Bacillota, and Actinomycetota. At the genus level, the genus Salmonella dominated the enterobacterial microbiota in the samples from Hainan, while there was no obvious dominant genus in the enterobacterial microbiota of the samples from the other four localities. Comparative analysis of enzyme families annotated to the gut microbiota between L. rufozonatus and L. rosozonatus from the four sampling regions by CAZy carbohydrate annotation revealed that nine enzyme families differed significantly in terms of glycoside hydrolases (GHs). In addition, we compared the composition of gut microbial communities between L. rufozonatus and L. rosozonatus and investigated the impact of the differences on their functions. Our results will provide insights into the coevolution of host and gut microbes.

Variations in the structure and function of the soil fungal communities in the traditional cropping systems from Madeira Island.

Agricultural soils are responsible for ecological functions and services that include primary production of food, fiber and fuel, nutrient cycling, carbon cycling and storage, water infiltration and purification, among others. Fungi are important drivers of most of those ecosystem services. Given the importance of fungi in agricultural soils, in this study, we aimed to characterize and analyse the changes of the soil fungal communities of three cropping systems from Madeira Island, where family farming is predominant, and investigate the response of fungi and its functional groups to soil physicochemical properties. To achieve that, we sequenced amplicons targeting the internal transcribed spacer 1 (ITS1) of the rRNA region, to analyse soil samples from 18 agrosystems: 6 vineyards (V), 6 banana plantations (B) and 6 vegetable plantations (H). Our results showed that alpha diversity indices of fungal communities are similar in the three cropping systems, but fungal composition and functional aspects varied among them, with more pronounced differences in B. Ascomycota, Basidiomycota, and Mortierellomycota were the main phyla found in the three cropping systems. Agaricomycetes and Sordariomycetes are the predominant classes in B, representing 23.8 and 22.4%, respectively, while Sordariomycetes (27.9%) followed by Eurotiomycetes (12.3%) were the predominant classes in V and Sordariomycetes (39.2%) followed by Tremellomycetes (8.9%) in the H. Saprotrophs are the fungal group showing higher relative abundance in the three cropping systems, followed by plant pathogens. Regarding symbionts, endophytes were highly observed in B, while mycorrhizal fungi was predominant in V and H. The structure of fungal communities was mainly correlated with soil content of P, K, N, Fe, and Cu. In addition, we identified bioindicators for each cropping system, which means that cultivated crops are also drivers of functional groups and the composition of communities. Overall, the three cropping systems favored diversity and growth of taxa that play important roles in soil, which highlights the importance of conservative management practices to maintain a healthy and resilient agrosystem.

Prevalence of antibiotic resistance genes, heavy metal, and bacterial community composition in sea sediments influenced by Eriocheir sinensis breeding aquaculture.

Eriocheir sinensis is the main aquaculture species in China. With the continuous expansion of the aquaculture scale, the demand for E. sinensis seedlings was also increased. The water used in breeding has well-nourished and its discharge into the sea posed significant risks. This study sampled the wastewater discharge points of the E. sinensis seedlings in Sheyang County, Jiangsu Province, and the areas far from the discharge points that were not affected in March and May 2023, respectively. A large number of antibiotic resistance genes (ARGs) were found in the sediment of the wastewater discharge area, and the highest ARG was sulfonamide ARG-sul1 using qPCR analysis, while ARGs were almost undetectable in the areas not affected by wastewater discharge. The 16S rRNA sequence analysis results showed that the main bacterial phyla at the wastewater discharge point were Bacteroidetes, Proteobacteria, and Thermodesulfobacteria. In the control point, the main bacterial phyla were Proteobacteria, Chlorobacterium, and Thermodesulfobacteria. There were significant differences in the composition of microbial communities between the two points, and the samples at the wastewater discharge point were more clustered and had higher similarity. The correlation network and redundancy analysis indicated that the phyla Bacteroidetes, Firmicutes, and Proteobacteria at the wastewater discharge points were positively correlated with most ARGs. The wastewater discharge had no effect on heavy metals from the two points. This study sets a foundation for future research by identifying key microbial taxa as potential ARG carriers and examining the interactions between microbial communities, ARGs, and heavy metals.

Microbial Community Structure and Metabolic Function in the Venom Glands of the Predatory Stink Bug, Picromerus lewisi (Hemiptera: Pentatomidae).

The predatory stink bug, Picromerus lewisi (Hemiptera: Pentatomidae), is an important and valuable natural enemy of insect pests in their ecosystems. While insects are known to harbor symbiotic microorganisms, and these microbial symbionts play a crucial role in various aspects of the host's biology, there is a paucity of knowledge regarding the microbiota present in the venom glands of P. lewisi. This study investigated the venom glands of adult bugs using both traditional in vitro isolation and cultural methods, as well as Illumina high-throughput sequencing technology. Additionally, the carbon metabolism of the venom gland's microorganisms was analyzed using Biolog ECO metabolic phenotyping technology. The results showed 10 different culturable bacteria where the dominant ones were Enterococcus spp. and Lactococcus lactis. With high-throughput sequencing, the main bacterial phyla in the microbial community of the venom glands of P. lewisi were Proteobacteria (78.1%) and Firmicutes (20.3%), with the dominant bacterial genera being Wolbachia, Enterococcus, Serratia, and Lactococcus. At the fungal community level, Ascomycota accounted for the largest proportion (64.1%), followed by Basidiomycota (27.6%), with Vishniacozyma, Cladosporium, Papiliotrema, Penicillium, Fusarium, and Aspergillus as the most highly represented fungal genera. The bacterial and fungal community structure of the venom glands of P. lewisi exhibited high species richness and diversity, along with a strong metabolism of 22 carbon sources. Functional prediction indicated that the primary dominant function of P. lewisi venom-gland bacteria was metabolism. The dominant eco-functional groups of the fungal community included undefined saprotroph, fungal parasite-undefined saprotroph, unassigned, endophyte-plant pathogen, plant pathogen-soil saprotroph-wood saprotroph, animal pathogen-endophyte-plant pathogen-wood saprotroph, plant pathogen, and animal pathogen-endophyte-epiphyte-plant pathogen-undefined saprotroph. These results provide a comprehensive characterization of the venom-gland microbiota of P. lewisi and demonstrate the stability (over one week) of the microbial community within the venom glands. This study represents the first report on the characterization of microbial composition from the venom glands of captive-reared P. lewisi individuals. The insights gained from this study are invaluable for future investigations into P. lewisi's development and the possible interactions between P. lewisi's microbiota and some Lepidopteran pests.

The dynamic changes and correlations between biochemical properties, flavor and microbial community during fermentation of asparagus by-products

Asparagus by-products are the promising resource that urgently need to be re-valorized. This study investigated the dynamic changes in physicochemical properties, organic acids, free amino acids, volatile flavor compounds, microbial succession, and their correlations during 7-day spontaneous fermentation of asparagus by-products. Dominant organic acids (lactic acid and acetic acid) and free amino acids (Ser, Glu, and Ala) increased with fermentation time, with lactic acid reaching 7.73 ± 0.05 mg/mL and Ser increasing 56-fold after 7 days. A total of 58 volatile flavor compounds were identified using headspace solid-phase microextraction-gas chromatography–mass spectrometry (HS-SPEM/GC–MS), with esters, alcohols and acids as the main volatile flavor compounds. Fourteen volatile flavor compounds had odor activity value >1. High-throughput sequencing showed Firmicutes and Proteobacteria as the main bacterial phyla, dominated by lactic acid bacteria (Levilactobacillus, Lactiplantibacillus, Weissella). Correlation analysis revealed that five bacterial genera (Levilactobacillus, Lactiplantibacillus, Enterobacter, Pediococcus and Acetobacter) were highly correlated with organic acids, free amino acids, and volatile flavor compounds, indicating their pivotal role in forming the characteristic flavor of fermented asparagus by-products (FAPS). This study provides new insights into the flavor and microbial profile of FAPS, offering a strategy for value-added processing and industrial production.

Effect of different vegetation restoration patterns on community structure and co-occurrence networks of soil fungi in the karst region.

The Grain for Green Project (GGP) by the Chinese government was an important vegetation restoration project in ecologically fragile and severely degraded karst regions. Soil fungi play a facilitating role in the cycling of nutrients both above and below the ground, which is crucial for maintaining ecosystem function and stability. In karst regions, their role is particularly critical due to the unique geological and soil characteristics, as they mitigate soil erosion, enhance soil fertility, and promote vegetation growth. However, little is known about how the implementation of this project shifts the co-occurrence network topological features and assembly processes of karst soil fungi, which limits our further understanding of karst vegetation restoration. By using MiSeq high-throughput sequencing combined with null model analysis technology, we detected community diversity, composition, co-occurrence networks, and assembly mechanisms of soil fungi under three GGP patterns (crop, grassland, and plantation) in the southwestern karst region. Ascomycota and Basidiomycota were the main fungal phyla in all the karst soils. Returning crop to plantation and grassland had no significant effect on α diversity of soil fungi (P > 0.05), but did significantly affect the β diversity (P = 0.001). Soil moisture and total nitrogen (TN) were the main factors affecting the community structure of soil fungi. Compared with crop, soil fungi networks in grassland and plantation exhibited a higher nodes, edges, degree, and relatively larger network size, indicating that vegetation restoration enhanced fungal interactions. The soil fungi networks in grassland and plantation were more connected than those in crop, implying that the interaction between species was further strengthened after returning the crop to plantation and grassland. In addition, null-model analysis showed that the assembly process of soil fungal communities from crop to grassland and plantation shifted from an undominant process to dispersal limitation. These data indicated that GGP in karst region changed the composition and assembly mechanisms of the soil fungal community and enhanced the interaction between fungal species, which can contribute to a better understanding of the fungal mechanisms involved in the restoration of degraded karst soils through vegetation recovery.

Harnessing next-generation sequencing to monitor unculturable pathogenic bacteria in the indoor hospital building

The hospital indoor air microbiome, a diverse range of microorganisms, gains prominence amid the COVID-19 pandemic. Elevated awareness underscores implications for patient and staff well-being. Concerns about risks to indoor air quality persist due to prolonged indoor exposure, necessitating further research on specific threats within the hospital environment. In this study, an independent culture-based approach was used to analyze the baseline core microbiome present in hospital environments, utilizing amplicon sequencing on the next-generation sequencing technology to target the V3 region of the 16S rRNA gene. Firmicutes, Proteobacteria, and Actinobacteria were the main bacterial phyla that were most isolated from the wards and clinics with different orders of abundance; Firmicutes being associated more in clinics and Actinobacteriota in wards. The bacteria Niallia taxi, Methyloversatilis universalis, unclassified Rummeliibacillus, unclassified Clostridium, and unclassified Sphingomonadaceae dominated the clinic area while ward areas reported Pseudonocardia bannensis, Rubrobacter aplysinae, unclassified Brachybacterium, unclassified Bradyrhizobium, and unclassified Mycobacterium to be the top five features. While the alpha-diversity index showed no significant differences, the beta-diversity analysis showed a significant difference between clinic and ward areas (p<0.05). Certain bacterial species associated with opportunistic pathogens as well as normal skin flora such as Methylobacterium spp., Cutibacterium spp., unclassified Sphingomonadaceae, and Anoxybacillus B spp., were also identified across all samples. The methods described in this research aim to establish a rapid and sensitive screening process that could be valuable for disease surveillance within the healthcare setting, shedding light on the potential impacts of the hospital microbiome on human illness.

Dynamic changes in and correlations between microbial communities and physicochemical properties during the composting of cattle manure with Penicillium oxalicum

BackgroundPenicillium oxalicum is an important fungal agent in the composting of cattle manure, but the changes that occur in the microbial community, physicochemical factors, and potential functions of microorganisms at different time points are still unclear. To this end, the dynamic changes occurring in the microbial community and physicochemical factors and their correlations during the composting of cattle manure with Penicillium oxalicum were analysed.ResultsThe results showed that the main phyla observed throughout the study period were Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Halanaerobiaeota, Apicomplexa and Ascomycota. Linear discriminant analysis effect size (LEfSe) illustrated that Chitinophagales and Eurotiomycetes were biomarker species of bacteria and eukaryote in samples from Days 40 and 35, respectively. Bacterial community composition was significantly correlated with temperature and pH, and eukaryotic microorganism community composition was significantly correlated with moisture content and NH4+-N according to redundancy analysis (RDA). The diversity of the microbial communities changed significantly, especially that of the main pathogenic microorganisms, which showed a decreasing trend or even disappeared after composting.ConclusionsIn conclusion, a combination of high-throughput sequencing and physicochemical analysis was used to identify the drivers of microbial community succession and the composition of functional microbiota during cattle manure composting with Penicillium oxalicum. The results offer a theoretical framework for explaining microecological assembly during cattle manure composting with Penicillium oxalicum.

Bacterial and Archaeal Communities in Erhai Lake Sediments: Abundance and Metabolic Insight into a Plateau Lake at the Edge of Eutrophication.

The littoral zones of lakes are potential hotspots for local algal blooms and biogeochemical cycles; however, the microbial communities within the littoral sediments of eutrophic plateau lakes remain poorly understood. Here, we investigated the taxonomic composition, co-occurrence networks, and potential functional roles of both abundant and rare taxa within bacterial and archaeal communities, as well as physicochemical parameters, in littoral sediments from Erhai Lake, a mesotrophic lake transitioning towards eutrophy located in the Yunnan-Guizhou Plateau. 16S rRNA gene sequencing revealed that bacterial communities were dominated by Proteobacteria, Bacteroidetes, and Chloroflexi, while Euryarchaeota was the main archaeal phylum. Co-occurrence network analysis revealed that keystone taxa mainly belonged to rare species in the bacterial domain, but in the archaeal domain, over half of keystone taxa were abundant species, demonstrating their fundamental roles in network persistence. The rare bacterial taxa contributed substantially to the overall abundance (81.52%), whereas a smaller subset of abundant archaeal taxa accounted for up to 82.70% of the overall abundance. Functional predictions highlighted a divergence in metabolic potentials, with abundant bacterial sub-communities enriched in pathways for nitrogen cycling, sulfur cycling, and chlorate reduction, while rare bacterial sub-communities were linked to carbon cycling processes such as methanotrophy. Abundant archaeal sub-communities exhibited a high potential for methanogenesis, chemoheterotrophy, and dark hydrogen oxidation. Spearman correlation analysis showed that genera such as Candidatus competibacter, Geobacter, Syntrophobacter, Methanocella, and Methanosarcina may serve as potential indicators of eutrophication. Overall, this study provides insight into the distinct roles that rare and abundant taxa play in the littoral sediments of mesotrophic plateau lakes.

A novel coupling process to replace the traditional multi-stage anammox process-sulfur autotrophic denitrification coupled anammox system.

A novel coupling process to replace the traditional multi-stage anammox process-sulfur autotrophic denitrification (SAD) coupled anaerobic ammonium oxidation (anammox) system was designed, which solved problems of nitrate produced in anammox process and low nitrate conversion rate caused by nitrite accumulation in SAD process. Different filter structures (SAD filter and anammox granular sludge) were investigated to further explore the excellent performance of the novel integrated reactor. The results of sequential batch experiments indicated that nitrite accumulation occurred during SAD, which inhibited the conversion of nitrate to dinitrogen gas. When SAD filter and anammox granular sludge were added to packed bed reactor simultaneously, the nitrate removal rate increased by 37.21% and effluent nitrite concentration decreased by 100% compared to that achieved using SAD. The stratified filter structure solved groove flow. Different proportion influence of SAD filter and anammox granular sludge on the stratified filter structure was evaluated. More suitable ratio of SAD filter to anammox granular sludge was 2:1. Proteobacteria (57.26%), Bacteroidetes (20.12%) and Chloroflexi (9.95%) were the main phyla. The dominant genera of denitrification functional bacteria were Thiobacillus (39.80%), Chlorobaculum (3.99%), norank_f_PHOs-HE36 (2.90%) and Ignavibacterium (2.64%). The dominant genus of anammox bacterium was Candidatus_Kuenenia (3.05%).

The biological contribution to the weathering of limestone monuments in a vegetated urban area: results of a 5-year exposure

Biological activity, climate and pollution are responsible for the degradation of building stones, especially limestone, which is widely used in the Paris region. In order to determine the respective contribution of physicochemical and biological processes to the degradation of limestone, limestone specimens from the Père-Lachaise cemetery (Paris, France) were exposed for five years under different conditions: sheltered from or exposed to rain and in horizontal or vertical position. After exposure, the collected samples were characterized by light and electron microscopy, X-Ray diffraction and ion chromatography after elution. The results showed an intense biocolonization of the samples exposed to rain, while the sheltered samples were more affected by the pollution (soiling). The characterization of the bacterial and fungal communities using Next Generation Sequencing Illumina 16S for bacteria and ITS for fungi highlighted that five main bacterial phyla were identified: Actinobacteriota, Bacteroidota, Cyanobacteria, Proteobacteria and Deinococcota (major genera Flavobacterium, Methylobacterium-Methylobacter, Sphingomonas, Roseomonas and Nocardiodes). Among the fungi, the phylum Ascomycota was predominant with the genera Cladosporium, Ramularia, Aureobasidium and Lecania. However, the alteration of the limestone is difficult to quantify at this stage. Potassium nitrate of rain origin has been found in the sheltered area, but no gypsum. Therefore, the biocolonization is a fast phenomenon on the stone and the physico-chemical processes derived from it, caused by climate and pollution, are slower. This is in agreement with the long-term observations made on old and unrestored graves of the cemetery described in the literature.

Microbiota composition effect on immunotherapy outcomes in colorectal cancer patients: A systematic review.

Immune checkpoint inhibitors (ICIs) have emerged as an effective treatment for colorectal cancer (CRC). Studies indicate that the composition of gut microbiota could potentially serve as a biomarker for predicting the clinical effectiveness of immune checkpoint inhibitors. Following PRISMA guidelines, the review was conducted after registering the protocol with PROSPERO. A comprehensive literature search was carried out across five databases: PubMed, Scopus, Web of Science, Embase, and Cochrane Library. Assessment tools from the National Institutes of Health (NIH) were used to gauge the quality of the studies. A total of 5,132 papers were identified, and three studies and one conference abstract published between 2017-2022 met the inclusion criteria and were summarized in a descriptive synthesis table. These four studies were in accord with the following findings, four main phyla, Firmicutes, Bacteroidata, Actinobacteria, and Verrucomicrobiota were associated with CRC patients' clinical response toward ICIs treatment. Ruminococcaceae was predominantly related to CRC patients responding to therapy, while the Micrococcaceae family was more common among the non-responders. Bacterial taxa such as Faecalibacterium and Prevotellaceae were associated with better responses to ICIs and could be predictive biomarkers. The signature of fecal microbiota with Akkermansia muciniphila and Eubacterium rectale enrichment, and Rothia mucilaginosa depletion could independently predict better response to ICIs in patients with CRC. The findings have brought attention to the notable differences in terms of richness and composition of microbiota between patients who responded positively to the treatment and those who did not. Bacterial species and families, such as Faecalibacterium, Bifidobacterium, Lachnospiraceae, Akkermansia sp., Ruminococcaceae, and Prevotellaceae, have consistently surfaced as potential indicators of immunotherapeutic responses. Furthermore, this review also emphasizes the need for additional comprehensive, multi-center studies with larger sample sizes to validate reported microbiota and expand our understanding of the role of gut microbiota in CRC ICIs therapy. PROSPERO ID: CRD42021277691.