Microbial Community Structure Research Articles

PSLBI-13 Characterizing the seminal microbiota in mature rams managed on divergent planes of nutrition, and in their male offspring

Abstract Increasing evidence suggests that the bovine semen harbors commensal microbiota, and it may be important in male fertility. However, much is unknown regarding the seminal microbiota, its evolution and factors shaping this community in sheep. The objective of this study was to evaluate whether managing the rams on divergent planes of nutrition can influence the seminal microbiota in mature rams and their male offspring. For this, Rambouillet rams (n = 24; 1.5 to 4 yr old) were randomly assigned to one of three groups: 1) a positive plane of nutrition [target 12% gain in their initial body weight (BW; POS, n = 8); 2) a maintenance [maintain the initial BW (MNT, n = 8)]; and 3) a negative [target a 12% reduction in BW (NEG; n = 8)] plane of nutrition over 84 d. The rams were individually housed and fed a common diet, and feed allocations were adjusted weekly. Following the 84-d feeding period, these rams were used to breed 240 mature Rambouillet ewes (1:10 ram:ewe ratio) over 28 d of breeding. After lambing, the male lambs were maintained on a similar diet for 124 d. Semen samples from the mature rams (F0 generation) were collected on d 28, 56, and 84, and semen samples from offspring rams (F1 generation) were collected at 330 d of age via electroejaculation. Genomic DNA was extracted from semen samples and the seminal microbiota characterized using 16S rRNA gene (V3-V4) sequencing. Several environmental and negative extraction controls were also sequenced to assess potential contaminants in these samples. Overall community structure of the seminal microbiota in F0 rams was not affected by the divergent planes of nutrition (PERMANOVA: P ≥ 0.05) or by sampling time (P > 0.05). Microbial richness (observed ASVs) was also not different (P > 0.05) between the three groups of F0 rams at any of the sampling time points; however, microbial diversity (P < 0.05) in the F0 rams was influenced by sire dietary treatment. Microbial community structure, richness and diversity did not differ among the POS, MNT and NEG F1 generation rams (P > 0.05). Actinobacteriota, Firmicutes, Bacteroidota, Proteobacteria and Fusobacteriota were the most abundant phyla. Only Bacteroidota abundance was significantly (P < 0.05) different between three F0 groups, with POS rams had greater (18.6%) of this phylum on d 28 as compared with MNT (2.1%) and NEG (5.1%). The predominant genera identified included Fastidiosipila, Corynebacterium, Trueperella, Arthrobacter, Dietzia, Bifidobacterium, Streptobacillus, Ornithinimicrobium, and Porphyromonas, and their relative abundance was not affected (P > 0.05) by the dietary treatment in F0 rams. Overall, rams managed on positive and negative planes of nutrition harbored similar seminal microbiota to control rams, and divergent nutrition also had no effect on the offspring ram seminal microbiota.

PSLBII-7 Meta-analysis of the whole-body microbiota in cattle

Abstract Distinctive and self-sustainable microbial communities are present along the digestive, respiratory, and reproductive tracts, as well as in the mammary gland, and mucosal surfaces of the eye and hoof in cattle. Although the taxonomic and functional features of each of these communities have been relatively well characterized, this has been largely limited to the microbiome of an individual organ/site. However, recent developments suggest the presence of core taxa shared across the gut, respiratory, and reproductive microbiotas in cattle, and there is a need for a more holistic evaluation of microbial communities in and on cattle. Here, we performed a meta-analysis using all publicly available bovine 16S rRNA gene datasets deposited since 2019 to provide a holistic view of the whole-body microbiota. In total, we retrieved 16S rRNA gene sequences from 6,215 samples (53 studies originating from 29 different anatomical sites within beef and dairy cattle from Africa, Asia, Europe, South America, and North America. The 29 different anatomical sites including gut (ruminal fluid, ruminal tissues, feces, ileum, jejunum, cecum, colon and duodenum), respiratory (nasal cavity, deep nasopharynx, trachea and lung tissue), and reproductive tracts (female: vagina, endometrium and uterus; male: semen and prepuce), as well as the mammary gland (udder, teat apex, teat barrel, teat canal), eye (conjunctiva, ocular fluid and ocular surface swab), blood, hoof, joints and liver. Microbial community structure was distinct among different sample types (PERMANOVA, P < 0.05). Microbial richness differed by sample type (P < 0.0001) with mucosal surfaces (e.g. udder, eye and feet) having the greatest microbial richness followed by the gut. The lungs, liver, joints, semen and prepuce had the least microbial richness. Microbial diversity was greatest in the microbiota of the colon, cecum, teat apex, ruminal tissue and duodenum (Shannon diversity index > 5) while the liver (1.5), joint (2.3), and prepuce microbiota (2.7) were the least diverse. Bacillota had the highest relative abundance among phyla in the majority of microbial communities except for in the blood, prepuce, trachea and nasal cavity (dominated by Pseudomonadota), and liver (dominated by Fusobacteriota). The relatively most abundant genera across all samples were Mycoplasma (12.9%), Prevotella (3.9%), Bacteroides (2.4%), Escherichia (2.1%), Fusobacterium (2.0%), Ruminococcaceae UCG-005 (1.9%), Streptococcus (1.8%), Rikenellaceae RC9 (1.6%), and Corynebacterium (1.4%). However, their relative abundance varied greatly by body site, with the ocular and respiratory system samples dominated by Mycoplasma. Fusobacterium was relatively most abundant in the liver and semen, Corynebacterium in the mammary gland-associated samples, Bacteroides in the gut, and Streptococcus in the lower reproductive tract microbiota. Overall, our meta-analysis provides a comprehensive evaluation of the multiple bacterial communities in and on cattle, which will be useful for harnessing the whole-body microbiome to improve animal health and productivity.

PSLBI-27 Rumen microbiome dynamics in feedlot steers receiving free-choice garlic-infused mineral supplements

Abstract Garlic (Allium sativum) in its dehydrated or distillate (garlic oil) form has been used as a feed additive owing to its insecticidal, antimicrobial, and organoleptic properties. Commercial mineral mixtures have been formulated to contain a low proportion of dehydrated garlic powder as a strategy to deter pest flies and increase mineral intake in cattle. As an antimicrobial, garlic powder has the potential to alter the rumen microbiome, with possible implications for feed digestibility and the growth performance of beef cattle. This study evaluated the effect of short-term feeding of a garlic-mineral mixture in feedlot steers receiving high-grain diets. Four groups of twenty steers [total = 80, ~14 mo old, body weight (BW) = 599 ± 32 kg] were randomly assigned to either a 5% garlic-mineral (5DGP) or plain mineral supplement (MS). The individual feed and mineral intakes of the steers were measured with an automatic feeding system. Feed and mineral supplements were tracked in different bunks for each group. Baseline rumen fluid samples were collected from all steers at the end of an acclimatization period before administering the trial supplements. Rumen samples were later collected from 10 steers in each group with the greatest mineral supplement intake over the trial period. Total DNA and RNA were extracted from all rumen samples and subjected to metagenomic and metatranscriptomic sequencing, respectively. None of the bacterial species with an overall relative abundance of greater than 0.1% were differentially abundant between the two supplement treatments, nor did the rumen microbial community structures differ between the two groups (PERMANOVA: R2 = 0.02, P = 0.43). Regardless of the dietary supplement, the rumen microbiome of the steers was dominated by uncultured Prevotella spp. (in addition to Prevotella lacticifex) as well as the uncharacterized UBA2810 sp900317945 and UBA2810 sp002351705. Overall, these results show that a 5DGP can be effectively administered to cattle without significantly disrupting the rumen microbiome.

Additives improve the fermentation quality, anthocyanin content, and biological activity of purple Napier grass silage.

Purple Napier grass (PNG), a widely used grass rich in anthocyanin, is commonly employed in the production of silage. However, there is currently limited research on the retention of anthocyanin with or without additives during ensiling. Therefore, this study aimed to investigate the effect of different additives (Lactiplantibacillus plantarum CCZZ1 (LP), glucose, acetic acid, and dried soybean curd residue) on fermentation quality, anthocyanin content, and microbial community structure of PNG silage. Ensiling PNG without additives led to poor fermentation quality and rapid degradation of anthocyanin, resulting in a decline in antioxidant activity and the persistence of harmful microorganisms with high relative abundance. The use of additives, especially LP, effectively increased the relative abundance of L. plantarum, enhancing fermentation quality, the retention of anthocyanin (up to 166% increase rate) and antioxidant activity, while reducing the relative abundance of harmful microorganisms during ensiling for 30 days. Additionally, prolonged ensiling negatively affected the preservation of anthocyanin. Based on both fermentation quality and bioactivity, PNG should be ensiled for 30 days with LP inoculation. The employment of additives, especially LP, improved the fermentation quality, anthocyanin retention, and microbial community structure in PNG silage. To optimize both fermentation quality and bioactivity, it is recommended that PNG be ensiled for 30 days with LP inoculation. © 2024 Society of Chemical Industry.

Seismic events as potential drivers of the microbial community structure and evolution in a paleo-ocean analog

Anthropogenic perturbations profoundly affect aquatic ecosystem microbiomes and associated ecological functions. Comparatively, the effects of geological stresses on microbiome composition and stability remain poorly explored. Here, we monitored the archaeal, bacterial and microeukaryotes community structure over an 8-years period in Lake Dziani Dzaha (Comoros archipelago), that experienced a major earthquake swarm mid-survey, providing a rare opportunity to investigate the aftermaths of seismo-volcanic events on microbiome. Our results revealed the sensitivity of the aquatic microbial community towards seismicity and associated environmental changes, that triggered a major shift in microbiome composition and abundance with persisting consequences on structure and richness of the microbial ecosystem. Our findings suggest that seismological perturbations could be major drivers of the microbial community structure in aquatic environments through cascading effects on environmental conditions. Over geological time scales, such events may have been significant yet underestimated forces driving diversification and evolution of microbial communities.

Oriented regulation of earthworm production and vermicompost quality by carbon bioavailability management

Vermicomposting is an efficient bioconversion technology for recycling nutrients from organic waste materials. The biodegradability of raw materials has a significant impact on the earthworm transformation product. However, the management of carbon bioavailability is often overlooked during the vermicomposting process due to the varying degradability of C-rich source in different organic waste. This research aims to investigate the impact of different bioavailable carbon compositions on vermicomposting and to develop a strategy for efficient carbon management. The study involved systematic vermicomposting using four different biodegradable carbon sources (pineapple peels, rice straw, tomato straw, and sawdust) with varying carbon‑nitrogen ratios (ranging from 24 to 42). The earthworm production and vermicompost quality were comprehensively evaluated, along with the influence of carbon components on microbial community structure. The results indicated that the optimal vermicomposting treatments were achieved at PCM24, RCM30, TCM30, and MCM30 treatments. Maintaining an approximate ratio of 1:(0.5–1.3) between available and recalcitrant carbon components based on the optimal carbon‑nitrogen ratio was found to be optimal for regulating vermicomposting products. Increasing the proportion of available carbon enhanced the quality of vermicompost fertilizer, while a higher proportion of recalcitrant carbon could improve earthworm biomass production efficiency. Labile carbon proportion I (LCP1) and available carbon component (ACC) were identified as key indicators in influencing the formation of microbial community structure. Different carbon compositions led to the specific development and formation of microbial communities, further resulting in significant variations in vermicompost quality under the mediation of microbes. This study, for the first time, clarifies the impact of vermicomposting performance and microbial community from the perspective of carbon bioavailability, which is of great significance for the oriented regulation the vermicomposting efficiency and product in practice.

Pipe material and natural organic matter impact drinking water biofilm microbial community, pathogen profiles and antibiotic resistome deciphered by metagenomics assembly

Biofilms in drinking water distribution systems (DWDSs) are a determinant to drinking water biosafety. Yet, how and why pipe material and natural organic matter (NOM) affect biofilm microbial community, pathogen composition and antibiotic resistome remain unclear. We characterized the biofilms’ activity, microbial community, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and pathogenic ARG hosts in Centers for Disease Control and Prevention (CDC) reactors with different NOM dosages and pipe materials based on metagenomics assembly. Biofilms in cast iron (CI) pipes exhibited higher activity than those in polyethylene (PE) pipes. NOM addition significantly decreased biofilm activity in CI pipes but increased it in PE pipes. Pipe material exerted more profound effects on microbial community structure than NOM. Azospira was significantly enriched in CI pipes and Sphingopyxis was selected in PE pipes, while pathogen (Ralstonia pickettii) increased considerably in NOM-added reactors. Microbial community network in CI pipes showed more edges (CI 13520, PE 7841) and positive correlation proportions (CI 72.35%, PE 61.69%) than those in PE pipes. Stochastic processes drove assembly of both microbial community and antibiotic resistome in DWDS biofilms based on neutral community model. Bacitracin, fosmidomycin and multidrug ARGs were predominant in both PE and CI pipes. Both pipe materials and NOM regulated the biofilm antibiotic resistome. Plasmid was the major MGE co-existing with ARGs, facilitating ARG horizontal transfer. Pathogens (Achromobacter xylosoxidans and Ralstonia pickettii) carried multiple ARGs (qacEdelta1, OXA-22 and aadA) and MGEs (integrase, plasmid and transposase), which deserved more attention. Microbial community contributed more to ARG change than MGEs. Structure equation model (SEM) demonstrated that turbidity and ammonia affected ARGs by directly mediating Shannon diversity and MGEs. These findings might provide a technical guidance for controlling pathogens and ARGs from the point of pipe material and NOM in drinking water.

Invasive Amaranthus spp. for heavy metal phytoremediation: Investigations of cadmium and lead accumulation and soil microbial community in three zinc mining areas

Amaranthus spp. are a group of strongly invasive and vigorous plants, and heavy metal phytoremediation using alien invasive Amaranthus spp. has been a popular research topic. In this study, the bioconcentration factor (BCF) and translocation factor (TF) of Amaranthus spp. were evaluated, focusing on the accumulation potential of cadmium (Cd) and lead (Pb) by plants from three different zinc mining areas, namely Huayuan (HYX), Yueyang (LYX), and Liuyang (LYX). The HYX area has the most severe Cd contamination, while the LYX area has the most apparent Pb contamination. The results showed that Amaranthus spp. had a strong Cd and Pb enrichment capacity in low-polluted areas. To elucidate the underlying mechanisms, we used high-throughput sequencing of 16S rRNA and internal transcribed spacer (ITS) regions to analyze rhizosphere bacterial and fungal communities in three areas. The results showed significant differences in the structure, function, and composition of microbial communities and complex interactions between plants and their microbes. The correlation analysis revealed that some key microorganisms (e.g., Amycolatopsis, Bryobacterium, Sphingomonas, Flavobacterium, Agaricus, Nigrospora, Humicola) could regulate several soil factors such as soil pH, organic matter (OM), available nitrogen (AN), and available phosphorus (AP) to affect the heavy metal enrichment capacity of plants. Notably, some enzymes (e.g., P-type ATPases, Cysteine synthase, Catalase, Acid phosphatase) and genes (e.g., ZIP gene family, and ArsR, MerR, Fur, NikR transcription regulators) have been found to be involved in promoting Cd and Pb accumulation in Amaranthus spp. This study can provide new ideas for managing heavy metal-contaminated soils and new ways for the ecological resource utilization of invasive plants in phytoremediation.

Effect of extracorporeal shock wave therapy on the microbial community in burn scars: retrospective case-control study.

The effectiveness of extracorporeal shock wave therapy (ESWT) has been demonstrated in various medical fields, including burn medicine. It promotes wound healing, improves blood flow, and modulates the inflammatory responses. The recovery speed and outcomes of skin diseases are influenced by the skin microbiome; however, studies examining the effects of specific treatments on the skin microbiome are lacking. This study investigated the impact of ESWT on the skin microbiome of burn patients, focusing on the microbial diversity and community structure within burn scars. In the retrospective case-control study, nineteen patients with burn scars were treated with ESWT, and changes in their skin microbiome were evaluated. ESWT was administered weekly for three months, and samples were collected from the ESWT-treated burn scars and untreated normal skin. Blood chemistry, and pain and itching scores were evaluated during sample collection. The collected samples were then subjected to 16S rRNA sequencing. Microbial community analysis was conducted using the QIIME2 and R packages. After ESWT, changes in alpha diversity indices were observed in burn scars. Faith phylogenetic diversity (P<0.05) and observed features (P<0.01) increased, whereas the evenness index decreased (P<0.01); no marked changes were noted in untreated skin. Beta diversity analysis showed stable microbial community structures in both the treated and untreated areas. A considerable increase in Micrococcus and Staphylococcus abundance was observed. Network analysis revealed a more open microbial network structure after ESWT, indicating adaptive changes in the microbial community. ESWT enhances microbial diversity and modifies microbial community structure in burn scars, promoting a more balanced and functionally supportive microbiome. ESWT aids in scar remodeling and positively influences skin microbiome dynamics, contributing to improved skin health and recovery.

Effects of alligator weed invasion on wetlands in protected areas: A case study of Lishui Jiulong National Wetland Park

Wetlands are one of the ecosystems most easily and severely invaded by alien species. Biological invasions can have significant impacts on local plant communities and ecosystem functioning. While numerous studies have assessed the impacts of biological invasions on wetlands, relatively few have been conducted in protected areas such as national wetland parks. We conducted a field survey to investigate the effects of the invasive herb Alternanthera philoxeroides (alligator weed) on the productivity and structure of plant communities and soil microbial communities in the Lishui Jiulong National Wetland Park in Zhejiang, China. We also examined the potential influence of the distance to the river edge on the impact of the alligator weed invasion. The alligator weed invasion significantly altered the plant community structure. It reduced the coverage of co-occurring plant species, including native (−31.2 %), invasive (−70.1 %), and non-invasive alien plants (−58.4 %). However, it increased species richness by 50 %, Pielou's evenness by 20 %, and Simpson's diversity index by 29.1 % for the overall plant community. Furthermore, within the community not invaded by alligator weed, increasing the distance to the river edge decreased the number of native plants by 57.0 % and the aboveground biomass of other invasive plants by 78.6 %. Contrary to expectations, no effects of the alligator weed invasion were observed on soil fungal and bacterial communities. Therefore, the impacts of the alligator weed invasion varied with spatial context and plant category, emphasizing the need to consider multiple scales and environmental factors when assessing the effects of invasive species on plant biodiversity. These insights enhance our understanding of plant invasions in wetlands and can guide the development of effective management strategies for these important ecosystems.

Microbial community structure of decayed trunks of Populus euphratica desert riparian forests in the lower Tarim River, Xinjiang, China

Rich microbial communities are associated with tree decay, and they markedly impact the degradation of tree species and material cycling within ecosystems. The native Populus euphratica forests along the lower Tarim River of China are mostly mature or over-mature, with many tree trunks exhibiting features of extensive cavity decay and slow regeneration. In this study, a growth cone was used to drill a wood core at varying degrees of decay, and 16S and internal transcribed spacer techniques were used to identify the microbial structure (fungi and bacteria) within the wood core. Changes in the trunk microbial community under varying decay conditions were also examined. For healthy, lightly decayed, and heavily decayed trunk, the dominant bacterial and fungal phyla were Firmicutes and Actinobacteria, Ascomycota, and Basidiomycota, respectively. As decay progressed, the alpha diversity index of the microbial community tended to decline. The maximum number of differential species was found in healthy trunks, where leaner discriminant analysis effect size (LEfSe) of fungi and bacteria revealed 1 and 15 different species, respectively. Species network analysis showed that interspecific linkages were more complex within bacterial communities than within fungal communities, with the complexity of fungal interspecific relationship increasing as decay progressed. The microbial communities of P. euphratica trunks differed significantly with the varying degrees of decay. Microbes such as Ralstonia may also play key roles in the decay process. In addition to providing a foundation for the sustainable management of desert riparian forests, investigating the mechanisms through which microbial communities influence the deterioration of P. euphratica trunks provides information about the general health of P. euphratica forests.

Intercropping in Coconut Plantations Regulate Soil Characteristics by Microbial Communities

Intercropping is a commonly employed agricultural technique that offers numerous advantages, such as increasing land productivity, enhancing soil health, and controlling soil-borne pathogens. In this study, Artemisia argyi, Dioscorea esculenta, and Arachis pintoi were intercropped with coconuts and compared with naturally growing weeds (Bidens pilosa), respectively. The regulatory mechanism of intercropping was examined by analyzing the variability in soil properties and microbial community structure across different intercropping modes and soil depths (0–20 cm, 20–40 cm, and 40–60 cm). The results indicate that intercropping can increase the diversity of soil bacteria and fungi. Moreover, as soil depth increases, the changes in microbial communities weaken. Intercropping reduced soil SOM and increased pH, which is directly related to the changes in the abundance of Acidobacteria in the soil. In various intercropping systems, the disparities resulting from intercropping with A. pintoi are particularly pronounced. Specifically, intercropping with A. pintoi leads to an increase in soil potassium and phosphorus levels, as well as an enhancement in the abundance of Bacillus sp., which plays a crucial role in the suppression of plant pathogenic fungi within the soil ecosystem. The results of the correlation analysis and structural equation modeling (SEM) suggest that the impacts of three intercropping systems on microbial composition and soil indicators exhibit considerable variation. However, a common critical factor influencing these effects is the soil phosphorus content. Furthermore, our findings indicate that intercropping resulted in lower soil nitrogen levels, exacerbating nitrogen deficiency and masking its impact on the microbial community composition.

Effects of anthropogenic activities on the microbial community diversity of Ologe Lagoon sediment in Lagos State, Nigeria.

The impact of pollution on the Ologe Lagoon was assessed by comparing physicochemical properties, hydrocarbon concentrations and microbial community structures of the sediments obtained from distinct sites of the lagoon. The locations were the human activity site (OLHAS), industrial-contaminated sites (OLICS) and relatively undisturbed site (OLPS). The physicochemical properties, heavy metal concentrations and hydrocarbon profiles were determined using standard methods. The microbial community structures of the sediments were determined using shotgun next-generation sequencing (NGS), taxonomic profiling was performed using centrifuge and statistical analysis was done using statistical analysis for metagenomics profile (STAMP) and Microsoft Excel. The result showed acidic pH across all sampling points, while the nitrogen content at OLPS was low (7.44 ± 0.085mg/L) as compared with OLHAS (44.380 ± 0.962mg/L) and OLICS (59.485 ± 0.827mg/L). The levels of the cadmium, lead and nickel in the three sites were above the regulatory limits. The gas chromatography flame ionization detector (GC-FID) profile revealed hydrocarbon contaminations with nC14 tetradecane > alpha xylene > nC9 nonane > acenaphthylene more enriched at OLPS. Structurally, the sediments metagenomes consisted of 43 phyla,75 classes each, 165, 161, 166 orders, 986, 927 and 866 bacterial genera and 1476, 1129, 1327 species from OLHAS, OLICS and OLPS, respectively. The dominant phyla in the sediments were Proteobacteria, Firmicutes, Actinobacteria, and Chloroflexi. The principal component ordination (PCO) showed that OLPS microbial community had a total variance of 87.7% PCO1, setting it apart from OLHAS and OLICS. OLICS and OLHAS were separated by PCO2 accounting for 12.3% variation, and the most polluted site is the OLPS.

Metagenomic analysis of soil from landfill site reveals a diverse microbial community involved in plastic degradation

In this study, we have investigated microbial communities structure and function using high throughput amplicon sequencing and whole metagenomic sequencing of DNA extracted from different depths of a plastic-laden landfill site. With diverse taxonomic groups inhabiting the plastic-rich soil, our study demonstrates the remarkable adaptability of microbes to use this new substrate as a carbon source. FTIR spectroscopic analysis of soil indicated degradation of plastic as perceived from the carbonyl index of 0.16, 0.72, and 0.44 at 0.6, 0.9 and 1.2 m depth, respectively. Similarly, water contact angles of 108.7 degree, 99.7 degree, 62.7 degree, and 77.8 degree of plastic pieces collected at 0.3, 0.6, 0.9, and 1.2 m depths respectively showed increased wettability and hydrophilicity of the plastic. Amplicon analysis of 16S and 18 S rRNA revealed a high abundance of several plastic-degrading bacterial groups, including Pseudomonas, Rhizobiales, Micrococcaceae, Chaetomium, Methylocaldum, Micromonosporaceae, Rhodothermaceae and fungi, including Trichoderma, Aspergillus, Candida at 0.9 m. The co-existence of specific microbial groups at different depths of landfill site indicates importance of bacterial and fungal interactions for plastic. Whole metagenome analysis of soil sample at 0.9 m depth revealed a high abundance of genes encoding enzymes that participate in the biodegradation of PVC, polyethylene, PET, and polyurethane. Curation of the pathways related to the degradation of these materials provided a blueprint for plastic biodegradation in this ecosystem. Altogether, our study has highlighted the importance of microbial cooperation for the biodegradation of pollutants. Our metagenome-based investigation supports the current perception that consortia of fungi-bacteria are preferable to axenic cultures for effective bioremediation of the environment.

Simultaneously reducing methane emissions and arsenic mobility by birnessite in flooded paddy soil: Overlooked key role of organic polymerisation

Flooding of paddy fields enhances methane (CH4) emissions and arsenic (As) mobilisation, which are crucial issues for agricultural greenhouse gas emissions and food safety. Birnessite (δ-MnO2) is a common natural oxidant and scavenger for heavy metals. In this study, birnessite was applied to As-contaminated paddy soil. The capacity for simultaneously alleviating CH4 emissions and As mobility was explored. Soil microcosm incubation results indicated that birnessite addition simultaneously reduced CH4 emissions by 47 %–54 % and As release by 38 %–85 %. The addition of birnessite decreased the dissolved organic carbon (DOC) contents and altered its chemical properties. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) results showed that birnessite reduced the labile fractions of proteins, carbohydrates, lignins, tannins, and unsaturated hydrocarbons, however, increased the abundance of condensed aromatic structures, suggesting the polymerisation of dissolved organic matter (DOM) by birnessite. The degradation of labile fractions and the polymerisation of DOM resulted in an inventory of recalcitrant DOM, which is difficult for microbes to metabolise, thus inhibiting methanogenesis. In contrast, birnessite addition increased CH4 oxidation, as the particulate methane monooxygenase (pmoA) gene abundance increased by 30 %. The enhanced polymerisation of DOM by birnessite also increased As complexation with organics, leading to the transfer of As to the organic bound phase. In addition, the decrease in ferrous ion [Fe(II)] concentrations with birnessite indicated that the reductive dissolution of Fe oxides was suppressed, which limited the release of arsenite [As(III)] under reducing conditions. Furthermore, birnessite decreased As methylation and shaped the soil microbial community structure by enriching the metal-reducing bacterium Bacillus. Overall, our results provide a promising method to suppress greenhouse gas emissions and the risk of As contamination in paddy soils, although further studies are needed to verify its efficacy and effectiveness under field conditions.

Legendary fermented herbs: an ethnobotanical study of the traditional fermentation starter of the Chuanqing people in Northwestern Guizhou, China

BackgroundPlants that contain brewing microorganisms are used in traditional fermentation starters, which are an essential part of local diet, nutrition, life, and health. Regionally, the plant species used and the microorganisms included in traditional fermentation starters are diverse, endowing local fermented drinks with different flavors and health benefits. However, related traditional knowledge has been scarcely documented or revealed.MethodsAn ethnobotanical survey was conducted in five towns of Nayong County in northwestern Guizhou, China. Snowball sampling, semi-structured interviews, free lists, and participatory observation were used to collect information on Jiuqu Plants (JPs) and jiuqu-making techniques. The PacBio platform was used to study the microbial community structure and diversity in the Chuanqing people’s jiuqu.ResultsIn total, 225 informants were interviewed, including 116 who provided plants and technological processes for making Chinese baijiu jiuqu (CBJ) and 139 who provided information about making fermented glutinous rice jiuqu (FGRJ). This study found that older people have more abundant knowledge about CBJ plants. Poaceae was found to be the dominant family used in making CBJ and FGRJ (7 species each). Compared to individual plant parts, the whole plant is most commonly used in two kinds of jiuqu (19.5% in CBJ and 22.6% in FGRJ). The Chuanqing people’s jiuqu is used to treat dietary stagnation and indigestion. The highest relative frequency of citation of the CBJ plant was Ficus tikoua Bureau, and the counterpart of the FGRJ plant was Buddleja macrostachya Benth. The dominant bacterial species in jiuqu were Gluconobacter japonicus (YQ1, YQ4) and Pediococcus pentosaceus (YQ2, YQ3), and the dominant fungal species was Rhizopus oryzae.ConclusionFor the first time, this study documents the unique traditional jiuqu knowledge and reveals the microbial mystery behind the FGRJ of the Chuanqing people.Therefore, this study encourages the use of online social media platforms in order to spread Jiuqu culture, the use of the new media wave in order to create multimedia databases, and also suggests that local communities should develop preservation intervention programs, in addition to nurturing the inheritors in order to prevent the disappearance of traditional Jiuqu knowledge. This research contributes to the conservation and demystification of the traditional jiuqu knowledge of the Chuanqing people and lays the foundation for further research on its microbiology, nutrition, and metabolomics.

Characterization of larval gut microbiota of two endoparasitoid wasps associated with their common host, Plutella xylostella (Linnaeus) (Lepidoptera: Plutellidae).

Insect gut microbes play important roles in digestion, metabolism, development, and environmental adaptation. Parasitoid wasps are one of the most important biological control agents in pest control, while the gut microbial species compositions and the associated functions have been poorly investigated. Two endoparasitoid wasps, Cotesia vestalis and Diadromus collaris, parasitize the larval stage and pupal stage of the diamondback moth, Plutella xylostella, respectively. Using whole-genome shotgun metagenomic sequencing, we characterized the gut microbial composition, diversity, and potential functional roles associated with the two parasitoid wasp larvae. The results reveal that Proteobacteria and Firmicutes are the dominant phyla in the gut of C. vestalis and D. collaris larvae, with Rhizobium and Enterococcus being the dominant genera. The putative microbial functions associated with the two parasitoid wasps might play a virtual role in assisting in consuming the host's nutritional composition. The enriched CAZymes family genes are primarily involved in the degradation and synthesis of chitin. Despite the richness of microbial species and communities, the microbes species and the microbial community structure exhibit significant similarity between the two parasitoid wasps and between the parasitoid wasp and the host P. xylostella. Notably, the prevalence of the genus Enterococcus shared among them suggests a possible link of gut microbes between the host and their associated parasitoids. Our study offers insights into the gut microbe-based interactions between the host and parasitoid wasps for the first time, potentially paving the way for the development of an ecologically friendly biocontrol strategy against the pest P. xylostella.IMPORTANCEEndoparasitoid wasps spend the majority of their lifespan within their host and heavily rely on the host's nutrition for survival. There is limited understanding regarding the composition and physiological impacts of gut microbial communities in parasitoid wasps, particularly during the larval stage, which is directly linked to the host. Based on a thorough characterization of the gut microbe and comprehensive comparative analysis, we found the microbial species of the larval parasitoid wasp Cotesia vestalis and the pupal parasitoid wasp Diadromus collaris were similar, sharing 159 genera and 277 species, as were the microbial community structure. Certain of the dominant microbial strains of the two parasitoid wasps were similar to that of their host Plutella xylostella larvae, revealing host insect may affect the microbial community of the parasitoid wasps. The putative microbial functions associated with the parasitoid wasp larvae play an important role in dietary consumption.

Sewage sludge fertilization affects microbial community structure and its resistome in agricultural soils

Global sewage sludge production is rapidly increasing, and its safe disposal is becoming an increasingly serious issue. One of the main methods of municipal sewage sludge management is based on its agricultural use. The wastewater and sewage sludge contain numerous antibiotic resistance genes (ARGs), and its microbiome differs significantly from the soil microbial community. The aim of the study was to assess the changes occurring in the soil microbial community and resistome after the addition of sewage sludge from municipal wastewater treatment plant (WWTP) in central Poland, from which the sludge is used for fertilizing agricultural soils on a regular basis. This study used a high-throughput shotgun metagenomics approach to compare the microbial communities and ARGs present in two soils fertilized with sewage sludge. The two soils represented different land uses and different physicochemical and granulometric properties. Both soils were characterized by a similar taxonomic composition of the bacterial community, despite dissimilarities between soils properties. Five phyla predominated, viz. Planctomycetes, Actinobacteria, Proteobacteria, Chloroflexi and Firmicutes, and they were present in comparable proportions in both soils. Network analysis revealed that the application of sewage sludge resulted in substantial qualitative and quantitative changes in bacterial taxonomic profile, with most abundant phyla being considerably depleted and replaced by Proteobacteria and Spirochaetes. In addition, the ratio of oligotrophic to copiotrophic bacteria substantially decreased in both amended soils. Furthermore, fertilized soils demonstrated greater diversity and richness of ARGs compared to control soils. The increased abundance concerned mainly genes of resistance to antibiotics most commonly used in human and animal medicine. The level of heavy metals in sewage sludge was low and did not exceed the standards permitted in Poland for sludge used in agriculture, and their level in fertilized soils was still inconsiderable.

The influence of urban environmental effects on the orchard soil microbial community structure and function: a case study in Zhejiang, China.

The urban environmental effects can have multifaceted impacts on the orchard soil microbial community structure and function. To specifically study these effects, we investigated the soil bacterial and fungal community in the laxly managed citrus orchards using amplicon sequencing. Ascomycota demonstrated significant dominance within the citrus orchard soils. The increased presence of beneficial Trichoderma spp. (0.3%) could help suppress plant pathogens, while the elevated abundance of potential pathogenic fungi, such as Fusarium spp. (0.4%), might raise the likelihood of disorders like root rot, thereby hindering plant growth and resulting in reduced yield. Moreover, we observed significant differences in the alpha and beta diversity of bacterial communities between urban and rural soils (p < 0.001). Environmental surveys and functional prediction of bacterial communities suggested that urban transportation factors and rural waste pollution were likely contributing to these disparities. When comparing bacterial species in urban and rural soils, Bacillus spp. exhibited notable increases in urban areas. Bacillus spp. possess heavy metal tolerance attributed to the presence of chromium reductase and nitroreductase enzymes involved in the chromium (VI) reduction pathway. Our findings have shed light on the intricate interplay of urban environmental effects and root systems, both of which exert influence on the soil microbiota. Apart from the removal of specific pollutants, the application of Bacillus spp. to alleviate traffic pollution, and the use of Trichoderma spp. for plant pathogen suppression were considered viable solutions. The knowledge acquired from this study can be employed to optimize agricultural practices, augment citrus productivity, and foster sustainable agriculture.

Water temperature disturbance alters the conjugate transfer of antibiotic resistance genes via affecting ROS content and intercellular aggregation

Spread of antibiotic resistance genes (ARGs) in aquatic ecosystems poses a significant global challenge to public health. The potential effects of water temperature perturbation induced by specific water environment changes on ARGs transmission are still unclear. The conjugate transfer of plasmid-mediated ARGs under water temperature perturbation was investigated in this study. The conjugate transfer frequency (CTF) was only 7.16 × 10−7 at a constant water temperature of 5 °C, and it reached 2.18 × 10−5 at 30 °C. Interestingly, compared to the constant 5 °C, the water temperature perturbations (cooling and warming models between 5–30 °C) significantly promoted the CTF. Intracellular reactive oxygen species was a dominant factor, which not only directly affected the CTF of ARGs, but also functioned indirectly via influencing the cell membrane permeability and cell adhesion. Compared to the constant 5 °C, water temperature perturbations significantly elevated the gene expression associated with intercellular contact, cell membrane permeability, oxidative stress responses, and energy driven force for CTF. Furthermore, based on the mathematical model predictions, the stabilization times of acquiring plasmid maintenance were shortened to 184 h and 190 h under cooling and warming model, respectively, thus the water temperature perturbations promoted the ARGs transmission in natural conditions compared with the constant low temperature conditions.