Microbial Community Structure Research Articles

Prescribed burning alters soil microbial community structure by changing soil physicochemical properties in temperate forests of northern China

Prescribed burning is commonly used to maintain forest ecosystem functions and reduce the risk of future wildfires. Although many studies have investigated the response of microbial community to wildfires in forest ecosystems, the effects of prescribed burnings on soil microbial community structure are less studied. It is also unclear that how post-fire soil physiochemical properties changes affected soil microbial communities. Here, we studied the impacts of prescribed burning on soil microbiome in three typical temperate forests of northern China by collecting soil physicochemical and high-throughput sequencing for 16S rRNA and 18S rRNA was applied to analyze the diversity and community composition of soil microbes (bacteria and fungi). Compared with pre-fire condition, prescribed burning significantly decreased Chao1 index and altered soil bacterial communities (P < 0.05), whereas it had no significant effect on fungal diversity and community structure of the (P > 0.05). Planctomycetes and Actinobacteria made the greatest contributions to the bacterial community dissimilarity between the pre-fire and post-fire conditions. The main variables influencing the post-fire soil microbial community structure are soil pH, available phosphorus, total nitrogen, and the ratio of soil total carbon to soil total nitrogen, which could account for 73.5% of the variation in the microbial community structure in these stands. Our findings demonstrated a great discrepancy in the responses of bacteria and fungi to prescribed burning. Prescribed burning altered the soil microbial structure by modifying the physicochemical properties. Our results pointed that it is essential to evaluate the impact of prescribed burnings on forest ecosystem functions. These findings provide an important baseline for assessing post-fire microbial recovery in the region and offer critical guidance for restoration efforts.

Effective elimination of internal phosphorus pollution with MgFe-LDHs hybrid material in eutrophic water: The chemical forms, transformation mechanism, and dynamic relationships

The internal phosphorus (P) pollution is a major cause of water eutrophication. Although the traditional powders materials, with good performance, were difficult to recycle due to its shape, and the reaction mechanism between materials and internal P was rarely elucidated. In this work, a hydrotalcite composite material (MgFe-LDHs hybrid gel microspheres) was prepared via chemical crosslinking to eliminate internal P pollution both in overlying water and sediments effectively. Benefiting from the strong coordination between iron hydroxide on the MgFe-LDHs surface and internal P, the P adsorption capacity was up to 1256.38 mg/kg under natural conditions, the IP (NaOH-P and HCl-P) and OP were 78 % and 22 %, respectively. During 40-days remediation experiment, with the addition of MgFe-LDHs hybrid gel microspheres, whatever in the mixed or the capped, promoted a conversion from stable P to soluble active P of NaOH-P in sediments, and thus contributing to an easy adsorption of NaOH-P by MgFe-LDHs hybrid gel microspheres (The NaOH-P in sediments decreased by 16 % and 22 %, respectively). Meanwhile, the excessive stable HCl-P (only a minor portion) that could not be adsorbed by MgFe-LDHs remained in the form of Ca-P in sediments. Additionally, the MgFe-LDHs hybrid gel microspheres improved the microbial community structure, and the microorganism was involved in the elimination of internal P simultaneously. In summary, this study proposed a promising remediation approach to resolve the problem of internal P pollution in eutrophic water with high efficiency, cost-effective, and environmentally friendly.

Biochar amendment affects the microbial genetic profile of the soil, its community structure and phospholipid fatty acid contents

Biochar (BC) amendment has been proposed as a promising strategy for mitigating greenhouse gas (GHG) emissions, specifically carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O). Conducting a meta-analysis to evaluate the impact of biochar on microbial genetic profile, community structure, and phospholipid fatty acid (PLFA) contents can aid in identifying key microbial groups involved in GHG production and consumption, and assessing the overall effectiveness of biochar in reducing GHG emissions. The present meta-analysis revealed that the addition of biochar resulted in a 22 % and 41 % reduction in pmoA and mcrA genes of methanogenic microorganisms, respectively. The mcrA/pmoA ratio significantly increased by 81 %. Gene abundances exhibited a positive response to biochar amendment, with increases observed in nifH, nirK, nirS, nosZ, and nosZ (nirS + nirK) genes by 13 %, 32 %, 37 %, 42 %, and 79 %, respectively. Moreover, biochar amendment influenced the microbial community structure accordingly. The concentration of PLFAs increased in response to BC treatment in the following order: A-bacteria (+49 %) < Fungi (+30 %) < Gram-pb (+21 %) < G-bacteria (+17 %) < Gram-nb (+11 %). These findings indicate that biochar amendment shapes the microbial community structure, further emphasizing its significance in enhancing soil fertility.

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

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

Comparative analysis of crop rotation systems: the impact of ginger (Zingiber officinale) and sponge gourd (Luffa aegyptiaca) residues on growth of Chinese cabbage (Brassica rapa var. chinensis).

Continuous cropping in greenhouse cultivation often leads to increased pest and disease problems, reducing crop quality and yield. Crop rotation is a common strategy to address these issues. This study compared the growth of Chinese cabbage (Brassica rapa var. chinensis) following rotations with ginger (Zingiber officinale) and sponge gourd (Luffa aegyptiaca). The Chinese cabbage exhibited normal growth following ginger rotation but showed abnormal growth after sponge gourd rotation. The study investigated the underlying causes by analyzing soil physicochemical properties and rhizosphere microbial communities of Chinese cabbage using 16S rRNA and ITS sequencing. The results revealed that soil from ginger-Chinese cabbage rotation had higher levels of soil organic carbon (SOC) and available phosphorus (AP), but lower total nitrogen (TN) and available potassium (AK). Despite similar alpha-diversity for both bacterial and fungal communities, distinct bacterial and fungal community structures between two rotation cropping systems were observed. This suggests that even if the alpha-diversity does not change, the composition of the microbial community can shift in ways that might influence soil health and plant growth. Furthermore, redundancy analysis revealed a significant correlation between microbial community structures and soil physicochemical properties of two rotation cropping systems. The SOC and TN were revealed to be the most significant of the investigated soil physicochemical parameters with respect to the variation of both bacterial and fungal assemblages, respectively. The identified biomarkers in bacterial community composition further emphasize the potential for specific microbes to influence crop health positively or negatively. We found that the indicator genera of the bacterial community composition of the ginger-Chinese cabbage rotation system were Amycolatopsis (genus), Pseudonocardiales (order), Pseudonocardiaceae (family), and Amycolatopsis mediterranei, which are known as producers of secondary metabolites, such as antibiotics. These findings highlight the importance of crop selection in rotation strategies for optimizing agricultural outcomes.

Safety and security of household water purifiers against pathogenic microbial contamination and bio-risk evaluation of their microbial community structures

Household water filters, particularly point-of-use systems, are crucial to ensure safe drinking water consumption by eliminating microbial contaminants. This study evaluated the efficacy of three types of water purifiers (ultrafiltration [UF], nanofiltration [NF], and reverse osmosis [RO]) against microbial contamination. In our experiments, Escherichia coli and bacteriophage MS2 were used as two microbial indicators in daily household settings to track the spatial and temporal profiles of their behavior from the filter inlets to in-UF, NF, and RO water purifiers, and then to effluents. The results showed that both NF and RO water purifiers removed 100 % of the indicator organisms. The UF water purifier achieved 100 % removal of E. coli, but the removal of MS2 phage was poor. The presence of coexisting ions and natural organic matter in tap water can significantly affect the behavior of MS2 phages during the water treatment process. Their presence reduces the charge repulsion effect of the UF membrane on the MS2 phage as well as promotes the migration of the MS2 phage on the post-activated carbon cartridge that was placed in the last unit of the water purifier system, which could increase the pathogen transmission risks in drinking water supplies. The bacterial community structures of the cartridge materials and cartridge effluents from each unit were analyzed by 16S rRNA gene sequencing, which revealed distinct microbial profiles of the different purifiers. Environmental conditions such as pH, nutrient availability, materials, and operational parameters can affect the composition of bacterial communities. Scanning electron microscopy-energy-dispersive X-ray spectroscopy (SEM-EDS) was used to examine the surface morphology of the membranes after they were exposed to water contaminants, which demonstrated that the inherent differences in the membrane structure influenced the retention of pollutants and microorganisms on the surfaces. In summary, this study demonstrates that both NF and RO water purifiers can significantly reduce the presence of various enteric and opportunistic pathogenic bacteria in drinking water, leading to safer potable water, whereas UF water purifiers may have certain risks owing to their UF membranes and post-activated carbon. In addition, secondary microbial contamination may be introduced by the post-activated carbon units of water purifiers, especially after long-term usage. Therefore, we concluded that addressing the secondary microbial pollution caused by post-activated carbon after prolonged use and long-term shutdown is essential for maintaining the safety and quality of drinking water.

Enhancement of repeated inoculation strategy with a domesticated bacterial consortium on the biodegradation of high-level crude oil in soil

Repeated inoculation of hydrocarbon degrading microbes should be powerful to improve the survival of inoculant, which is vital to achieve efficient remediation of petroleum contaminated soil. This paper aims to study the repeated inoculation (with different inoculum size and time interval) enhanced bioremediation of high-level petroleum contaminated soil with a domesticated bacterial consortium. The copy number of bacterium and alkB gene, soil enzyme activities and microbial community structure during the remediation were systematically analyzed to preliminarily reveal the mechanism of repeated inoculation affecting remediation for the first time. The results revealed that repeated inoculation remarkably improved the total petroleum hydrocarbon (TPH) removal in soil (86.5 % in HC120) compared with a single inoculation (68.9 % in HA120). The TPH removal of repeated inoculation with high inoculum size (HC) on the 60th day was close to that of once inoculation (HA) on the 120th day, suggesting that repeated inoculation led to faster degradation. Interestingly, the effect of inoculation with low dose and more times (LC120, 78.5 %) was equal to that with high dose and less times (HB120, 78.0 %), even much better than that with high dose and once inoculation (HA120). Treatment HC had a significant impact on the soil bacterial diversity and community structure, and the dominant species in the inoculants, such as Stenotrophomonas and Pseudomonas, which was low abundance in the blank group (CK), still maintained high abundance during the remediation process. The soil catalase activities and the number of alkB gene were the highest in HC. Correlation analysis implied that repeated inoculation of hydrocarbon degrading bacteria did improve the survival of inoculant, soil enzyme activities and maintain the number of degrading bacteria, thus promoting the TPH removal. These findings will facilitate the practical application of bioremediation technology to contaminated environment, which has important environmental and economic benefits.

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

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

Effect of Sod Production on Physical, Chemical, and Biological Properties of Soils in North and South China

Lawns play a vital role in urban development, but the impact of sod production on soil properties has always been controversial. In this study, we examined the physical, chemical, and biological properties of sod production bases across different regions and years [including northern China (2.5, 3, 5, 6, 8, 10, 12 years), referred to as N-2.5, N-3, etc., and southern China (3, 10, 11, 14, 17 years), referred to as S-3, S-10, etc.], with tall fescue and Kentucky bluegrass planted in the north and bermudagrass or creeping bentgrass planted in the south. Sod production was found to increase soil bulk density while reducing porosity and field capacity, but these effects did not consistently intensify with longer production periods. Except for available phosphorus and available potassium, other soil nutrients (total carbon, total nitrogen, organic matter, alkali-hydrolyzable nitrogen, etc.) were either unaffected or increased at certain time points (S-11, S-14). Prolonged sod production (S-10, S-17) also boosted microbial content. In northern regions, organic matter and total nitrogen were the key factors influencing microbial community structure, whereas in southern regions, alkali-hydrolyzable nitrogen, electrical conductivity, available potassium, and organic matter were most influential. We also found that crop rotation, sand mulching, and deep plowing could enhance soil nutrient content and microbial activity in sod production.

Trichoderma Rhizosphere Soil Improvement: Regulation of Nitrogen Fertilizer in Saline–Alkali Soil in Semi-Arid Region and Its Effect on the Microbial Community Structure of Maize Roots

In order to reduce the actual impact of a saline–alkali environment on maize production in semi-arid areas, it is particularly important to use the combined fertilization strategy of Trichoderma microbial fertilizer and nitrogen fertilizer. The purpose of this study was to investigate the effects of different concentrations of nitrogen fertilizer combined with Trichoderma on improving the structural characteristics and ecological functions of maize rhizosphere microbial community in semi-arid saline–alkali soil. Through the microbiome analysis of maize rhizosphere soil samples with 60 kg N·ha−1 (N1) and 300 kg N·ha−1 (N2) nitrogen fertilizer combined with Trichoderma (T1) and without Trichoderma (T0), we found that the combination of Trichoderma and different concentrations of nitrogen fertilizer significantly affected the structure of bacterial and fungal communities. The results of this study showed that the combination of Trichoderma and low-concentration nitrogen fertilizer (N1T1) could improve soil nutritional status and enhance its productivity potential, revealing the relationship between beneficial and harmful fungal genera, microbial diversity and abundance, and crop biomass, which is of great significance for improving agricultural production efficiency and sustainable development.

Soil function-microbial diversity relationship is impacted by plant functional groups under climate change

Understanding the interactions between plant and soil microbial diversity is crucial for predicting ecosystem responses to environmental changes. While the individual roles of plant and microbial diversity in driving ecosystem functions have been widely investigated, their interplay especially under stress conditions remains largely underexplored. This study investigated how interactions between plant and microbial diversity affect key soil functions during and after drought. We simultaneously manipulated soil microbial diversity and plant species richness, while also considering the influence of plant functional groups (PFGs), to investigate their interactions and effects on key soil functions. Our results revealed independent and interactive effects of plant and microbial diversity in shaping soil functions. Microbial diversity loss significantly altered microbial community structure and impacted microbially-driven soil N and P pools and processes such as N-mineralization. These effects were modulated by plant species richness and varied across different PFGs. The relative influence of plant and microbial diversity on soil functions was context-dependent. Microbial diversity showed stronger effects on specific functions, such as phosphatase activity, and under the drought condition. Plant diversity, particularly through PFGs (e.g. legumes), played an independent role in shaping the microbial-driven soil functions. These findings advance mechanistic insights and highlight the importance of considering both above- and belowground biodiversity, along with their interactions, in shaping soil functions and ecosystem resilience, particularly under environmental stress. Further, it emphasizes the need to explicitly consider PFGs, along with above- and belowground biodiversity, as a strategy for preserving essential belowground functions in the face of ongoing environmental changes.

Stimulating Acidimicrobium sp. Strain A6 in iron-rich, acidic sediments from AFFF-impacted sites for PFAS defluorination

Per- and polyfluoroalkyl substances (PFAS) are persistent and bioaccumulative contaminants that are widely used in industrial applications and consumer products and pose significant risks to ecosystems and human health. Acidimicrobium sp. Strain A6 (A6), which is common in acidic, and iron rich soils and sediments is capable of both anaerobic ammonium (NH4+) oxidation under iron reduction (Feammox) and defluorination of perfluorinated alkyl substances, such as perfluoroalkyl acids (PFAAs). This study investigates the potential for biostimulating A6 via the supply of NH4+ and ferric iron (Fe(III)) with the goal of defluorinating PFAAs. Sediment samples from acidic, iron-rich, AFFF (aqueous film forming foam) impacted sites were collected and incubated with added Fe(III) and NH4+. Quantitative PCR was used to track A6 numbers as well as dehalogenase and F− ion transporter genes during these incubations; changes in the microbial community structure were tracked through 16S rRNA gene sequencing. The findings reveal that the addition of Fe(III) and NH4+ stimulated the Feammox reaction and A6 growth and enhanced the degradation of perfluorooctanoic acid (PFOA) and perfluorooctane sulfonic acid (PFOS). Results also show a significant presence and activity of the above-mentioned genes in these incubations. The insights gained from this study could inform bioremediation strategies for PFAS-contaminated environments, especially in geochemical settings that favor the presence of A6.

Spatial distribution of bacterial communities driven by environmental factors in the sediment of Lateolabrax japonicus ponds

Dynamic changes of bacterial communities in the sediment are very important for preventing diseases and water quality in aquaculture ponds. In this study, bacterial communities in the sediment of Sea perch Lateolabrax japonicus, an important farmed fish in China, ponds were studied using 16S rRNA Illumina sequencing and functional gene array. At the phylum level, Pseudomonadota, Actinomycetota and Chloroflexota were the dominant species. The bacterial community composition was different in spatial variation. Among the environmental factors, the concentration of nitrogen related factors (TN, NO3−-N NH3-N, NO2−N) and total organic carbon was the main impact on the composition of bacterial community, especially denitrifying bacterial community. Nitrifying and denitrifying bacteria accounted for 4.81 %, and bacteria related to nitrogen cycle accounted for 18.36 %. Higher diversity of bacteria in healthy fish pond than that of the diseased fish pond. In the diseased fish pond, lower abundance of Nitrosospira and higher abundance of Nitrobacter were found, and the contents of NH3-N, NO2−-N and total organic carbon were significantly higher. This study would help to reveal that microbial community structure could reflect the health of cultured animal and surroundings, and it could provide a theoretical reference for the healthy environments in the sediment of Sea perch ponds in South China.

Cadmium immobilization by mercapto-palygorskite in alkaline soil: Impacts on soil microbial communities and wheat rhizosphere metabolism

Weakly alkaline cadmium (Cd) contaminated soil in China has aroused great concern regarding its impact on food security and human health. Mercapto-modified palygorskite (MP) has exhibited good potential to minimize Cd accumulation in wheat, it is imperative to understand the underlying mechanisms within the soil-wheat-microbial system for sustainable development of agrochemicals. This study evaluated the effects of various MP dosages on soil Cd bioavailability, rhizosphere metabolomics, microbial community structure and wheat growth. The results indicated that MP (0.05–0.2 %) application significantly reduced Cd accumulation in wheat grains by 59.0–83.2 % (p < 0.05) and inhibited Cd translocation from root to grain. MP also promoted Mn oxide formation and redistributed the exchangeable Cd to Fe–Mn oxide-bound forms (44.2–109.6 %), thus lowering soil Cd bioavailability by 17.9–32.5 %. Additionally, MP reduced wheat rhizosphere organic acid levels, altered rhizosphere carbon and nitrogen pools, and stimulated the growth of Cd-tolerant Alternaria and Cladosporium, while inhibiting the growth of Fusarium. These findings highlight the potential of MP to modulate soil rhizosphere metabolism and microbial communities, offering a novel perspective on its environmental implications and supporting agrochemical sustainability.

Are Changes Occurring in Bacterial Taxa Community and Diversity with the Utilization of Different Substrates within SIR Measurements?

This research explores how the availability of substrates affects the regulation of soil microbial communities and the taxonomical composition of bacteria. The goal is to understand the impact of organic matter and substrate availability and quality on the diversity of soil bacteria. The study observed gradual changes in bacterial diversity in response to the addition of different substrate-induced respiration (SIR) substrates. Understanding the structure, dynamics, and functions of soil microbial communities is essential for assessing soil quality in sustainable agriculture. The preference for carbon sources among bacterial phyla is largely influenced by their life history and trophic strategies. Bacterial phyla like Proteobacteria, Bacteroidetes, and Actinobacteria, which thrive in nutrient-rich environments, preferentially utilize glucose. On the other hand, oligotrophic bacterial phyla such as Acidobacteria or Chloroflexi, which are found in lower numbers, have a lower ability to utilize labile C. The main difference between the two lies in their substrate utilization strategies. Understanding these distinct strategies is crucial for uncovering the bacterial functional traits involved in soil organic carbon turnover. Additionally, adding organic matter can promote the growth of copiotrophic bacteria, thus enhancing soil fertility.

Circadian rhythms of microbial communities and their role in regulating nitrogen and phosphorus cycling in the rhizosphere of tea plants

Abstract The circadian clock mediates metabolic functions of plants and rhythmically shapes structure and function of microbial communities in the rhizosphere. However, it is unclear how the circadian rhythm of plant hosts regulates changes in rhizosphere bacterial and fungal communities and nutrient cycles. In the present study, we measured diel changes in the rhizosphere of bacterial and fungal communities, and in nitrogen (N) and phosphorus (P) cycling in 20-year-old tea plantations. The fungal communities were more stable in their responses to circadian changes than bacterial communities in the rhizosphere of the variants LJ43 and ZC108. Nevertheless, fungal genera with circadian rhythms were more numerous and had a higher abundance at midnight. Organic P and N mineralization in the rhizosphere was more intensive in LJ43 under day-night alterations, while inorganic N and P cycling were more easily affected by circadian rhythms in ZC108. The rhizosphere denitrification encoded by the genes AOA and AOB was intensive in the morning, irrespective of tea species. Genes related to rhizosphere N fixation (nifH) and denitrification (nosZ and nirK) expressed at greater levels in ZC108, and they reached a peak at midnight. Moreover, the diel rhythm of rhizosphere microbial communities in ZC108 largely regulated dial changes in N and P cycling. These results suggested that the bacterial and fungal communities in the rhizosphere respond differently to circadian rhythms, and they vary between tea species. The timing of bacterial and fungal cycling largely regulates rhizosphere N and P cycling and their ecological functions.

Altitudinal variation in rhizosphere microbial communities of the endangered plant Lilium tsingtauense and the environmental factors driving this variation.

Our study highlighted the importance of the rhizosphere microbial community of the endangered plant L. tsingtauense. We found that soil pH plays an important role in the survival of L. tsingtauense. Our results demonstrated that a series of microbial taxa (Acidobacteriales, Xanthobacteraceae, Aspergillaceae, and Chaetomiaceae) and soil metabolites (phosphatidylcholine and phosphatidylserine) could be essential indicators for L. tsingtauense habitat. We also found that some environmental factors play an important role in shaping rhizosphere microbial community structure. Collectively, these results provided new insights into the altitudinal distribution of L. tsingtauense and highlight the importance of microbial communities in their growth.

Phage communities in household-related biofilms correlate with bacterial hosts

The average American spends 93% of their time in built environments, almost 70% of that is in their place of residence. Human health and well-being are intrinsically tied to the quality of our personal environments and the microbiomes that populate them. Conversely, the built environment microbiome is seeded, formed, and re-shaped by occupant behavior, cleaning, personal hygiene and food choices, as well as geographic location and variability in infrastructure. Here, we focus on the presence of viruses in household biofilms, specifically in showerheads and on toothbrushes. Bacteriophage, viruses that infect bacteria with high host specificity, have been shown to drive microbial community structure and function through host infection and horizontal gene transfer in environmental systems. Due to the dynamic environment, with extreme temperature changes, periods of wetting/drying and exposure to hygiene/cleaning products, in addition to low biomass and transient nature of indoor microbiomes, we hypothesize that phage host infection in these unique built environments are different from environmental biofilm interactions. We approach the hypothesis using metagenomics, querying 34 toothbrush and 92 showerhead metagenomes. Representative of biofilms in the built environment, these interfaces demonstrate distinct levels of occupant interaction. We identified 22 complete, 232 high quality, and 362 medium quality viral OTUs. Viral community richness correlated with bacterial richness but not Shannon or Simpson indices. Of quality viral OTUs with sufficient coverage (614), 532 were connected with 32 bacterial families, of which only Sphingomonadaceae, Burkholderiaceae, and Caulobacteraceae are found in both toothbrushes and showerheads. Low average nucleotide identity to reference sequences and a high proportion of open reading frames annotated as hypothetical or unknown indicate that these environments harbor many novel and uncharacterized phage. The results of this study reveal the paucity of information available on bacteriophage in indoor environments and indicate a need for more virus-focused methods for DNA extraction and specific sequencing aimed at understanding viral impact on the microbiome in the built environment.

Exotic mangrove Laguncularia racemosa litter input accelerates nutrient cycling in mangrove ecosystems.

Exotic plant litter presents different chemical and physical properties relative to native plant litter and alters ecosystem processes and functions that may facilitate exotic plant dispersal. However, these effects are largely unknown, especially within wetland ecosystems. This study examines whether introducing litter from theexotic mangrove Laguncularia racemosa could result in (1) accelerated community litter decomposition rates and increased nutrient cycling rates and (2)microbial community structure changes in the invaded areas. A single decomposition experiment using litterbags was conducted to examine the short-term effects of L. racemosa litter in the native mangrove forest ecosystem. The soil nutrients and microbial communities of Rhizophora stylosa, L. racemosa, and mixed forests were also compared to explore the long-term cumulative effects of L. racemosa litter in native ecosystems. The results indicated that L. racemosa has lower-quality leaf litter than R. stylosa and a significantly faster decomposition rate. This may result from changes in the soil microbial community structure caused by L. racemosa leaf litter input, which favors the decomposition of its own litter. Both the short-term and cumulative effect experiments demonstrated that L. racemosa leaf litter significantly increased the relative abundance of microbes related to litter decomposition, such as Proteobacteria and Bdellovibrionota, and enhanced the alpha diversity of soil fungi, thus creating a microbial environment conducive to L. racemosa leaf litter decomposition. Moreover, the accumulation of soil nutrients was lower under L. racemosa than under R. stylosa over several years. This may be related to the more rapid growth of L. racemosa, which causes soil nutrient absorption and storage within the plant tissues, thereby reducing the soil nutrient content. Inputting exotic mangrove L. racemosa leaf litter reduced the soil blue carbon content, potentially adversely affecting global climate change. L. racemosa may employ a unique strategy to lower soil nutrient levels in native mangroves based on its low-quality leaf litter, thereby weakening the competitive ability of native plants that are intolerant to low-nutrient conditions and enhancing its own competitive advantage to further spread into these areas. In summary, the input of exotic L. racemosa leaf litter accelerates nutrient cycling in local mangroves.

Antibiotic resistance genes are transferred from manure-contaminated water bodies to the gut microbiota of animals through the food chain

Fecal-contaminated water may enter the food chain and become an important route for the transmission of antibiotic resistance genes (ARGs) to the human microbiome. However, little is known about the spread of ARGs from fecal contamination in water bodies along the aquatic food chain. In this study, laboratory-raised Daphnia magna and Aristichthys nobilis were used to investigate the effects of the addition of manure on target ARGs in water and their intestinal contents to determine the potential transmission route of ARGs in the aquatic food chain system. The abundance of target ARGs in water as well as D. magna and A. nobilis intestinal contents significantly increased when fecal contamination was present. ARGs bioaccumulated along the food chain, with four ARGs (tetM-01, tetX, qnrS, and sul2) detected regularly. Mn and Cr were key environmental factors that promoted the transfer of ARGs along the food chain. Fecal addition significantly changed the structure of microbial communities in water, D. magna gut, and A. nobilis gut. The ARG spectrum was significantly correlated with the composition and structure of the bacterial community. Proteobacteria, Bacteroidetes, and Firmicutes were identified as the main host bacteria and were likely to act as carriers of ARGs to promote the spread of antibiotic resistance in the food chain. The composition and structure of bacterial communities, along with mobile genetic elements, were two key drivers of ARG transfer. These findings provide new insights into the distribution and spread of ARGs along the freshwater food chain.