Bacterial Community Richness Research Articles

Metagenomic analysis of microbial community and metabolic pathway of simultaneous sulfide and nitrite removal process exposed to divergent hydraulic retention times

The role of hydraulic retention time (HRT) on S0 production was assessed through metagenomics analyses. Considering comprehensive performance for the tested HRTs (0.25–13.33 h), the optimal HRT was 1 h, while respective sulfide and nitrite loading rate could reach 6.84 kg S/(m3·d) and 1.95 kg N/(m3·d), and total S0 yield was 0.36 kg S/(kg (VSS)·d). Bacterial community richness decreased along the shortening of HRT. Microbacterium, Sulfurimonas, Sulfurovum, Paracoccus and Thauera were highly abundant bacteria. During sulfur metabolism, high expression of sqr gene was the main reason of maintaining high desulfurization load, while lacking soxB caused the continuous increase of S0. Regarding nitrogen metabolism, the rapid decrease of nitrite transporter prevented nitrite to enter in cells, which caused a rapid decrease of nitrite removal under extreme HRT. Adjusting HRT is an effective way to enhance S0 production for the application of the simultaneous sulfide and nitrite removal process.

Soil bacteria around a derelict tailings pile with different metal pollution gradients: community composition, metal tolerance and influencing factors.

Bacteria play a vital role in ecological processes of soil contaminated by heavy metals. Here, soil sampling was carried out around a tailings pile contaminated to different degrees by cadmium (Cd), lead (Pb) and arsenic (As). The bacteria in the soil were cultured, separated and purified on Luria-Bertani medium, and the changes in bacterial communities in soils with different pollution levels were analysed with 16S rRNA sequencing. Bacillus pacificus strain MZ520364 was found to be highly tolerant to Cd, Pb and As, and single-metal and multimetal tolerance experiments were further conducted with this strain. The results obtained from alpha diversity and operational taxonomic unit (OTU) statistical analyses showed a significant difference in bacterial composition among soils with different metal pollution levels, and the highest bacterial diversity was found at the most severely polluted site. Evidence from variance partitioning analysis (VPA) and the Spearman correlation heatmap analysis showed that the leading factors affecting bacterial community composition were cation exchange content (CEC), pH, total Zn, total As, and available As concentrations in soil. Additionally, in the single-metal treatments, B. pacificus MZ520364 could tolerate 600mg/L Cd2+, 1000mg/L Pb2+ or 700mg/L As3+. When Cd, Pb and As coexisted, the best growth of B. pacificus MZ520364 was present at 120mg/L Cd2+, 200mg/L Pb2+ and 150mg/L As3+. The effect of Cd, Pb and As on the growth of the strain followed the order of Cd > As > Pb, and the heavy metal combination showed more toxicity than single metals. In summary, our results revealed the ecological impact of soil physicochemical properties on the diversity and richness of soil bacterial communities and suggested that B. pacificus MZ520364 may be used for the remediation of Cd-Pb-As co-contaminated soil.

Characteristics of airborne bacterial communities across different PM2.5 levels in Beijing during winter and spring

Airborne bacteria are important components of fine particulate matter (PM2.5), and have received increasing attention because of their impacts on public health and ecological systems. However, the relationships between the bacterial community and PM2.5 pollution are poorly understood. The properties of bacterial communities in Beijing at low, medium and high PM2.5 levels were analyzed during winter (December 2015–January 2016; January 2017) and spring (March 2016–May 2016; April 2017–May 2017). Variations in bacterial concentrations, Shannon and Simpson indices and relative abundance were significantly related to the seasons. In winter, there were no significant differences in bacterial communities among three PM2.5 pollution levels. In contrast, significant correlations between bacterial abundance and PM2.5 levels were observed in spring, and the bacterial concentrations, community richness and diversity indices were significantly higher on heavily polluted days compared to other pollution levels. Correlation results showed that relative humidity (RH), wind speed (WS), and O3 were most closely associated with microbial community structure in winter (P < 0.05), but temperature (T), NO2, SO2, and CO in spring, while CO, NO2, O3, RH, and WS had significant relationships (|r| = 0.360–0.553, P < 0.05) with bacterial concentrations in winter, but PM2.5, O3, T, and RH (|r| = 0.281–0.527, P < 0.05) in spring. Chemical composition, especially that of secondary aerosol particles, which were mainly produced from anthropogenic sources (e.g. fossil fuel combustion, road traffic and industrial emissions), exerted the most control of bacterial community structure of PM2.5. The effects of PM2.5 levels on the bacterial community were modified by environmental conditions, heavy metal and nutrient contents of the PM2.5. The relationships described provide a foundation for further research into the environmental and PM2.5 chemical composition controls on the bacterial community and related health risk from air pollution.

Effect of rice straw biochar on three different levels of Cd-contaminated soils: Cd availability, soil properties, and microbial communities

Biochar can be effective in immobilizing soil cadmium (Cd), but the difference in its immobilization mechanisms for different levels of Cd-contaminated soils was overlooked. In this study, rice straw biochar (BC) was added to three Cd-contaminated soils following 180 days of incubation, in the process of which the dynamic changes of Cd speciation, soil properties and microbial community diversity were determined. BC could significantly reduce the ratio of acid-soluble in the three soils, especially in light and medium Cd-contaminated soils by more than 20%. The addition of biochar could significantly increase the soil pH, soil organic matter, cation exchange capacity, and the activities of catalase, but decrease the richness and diversity of bacterial communities in all soils. The associations between microbial communities were inhibited in light and medium Cd-contaminated soils, but promoted in heavy Cd-contaminated soils. Furthermore, the main pathway of BC effect on soil Cd availability was also analyzed by partial least squares model (PLS-PM), which indicated that BC indirectly reduced Cd availability mainly by regulating the microbial community in light Cd-contaminated soil, whereas BC directly reduced Cd availability primarily by its own adsorption in medium and heavy Cd-contaminated soils. This research deepened understanding of the mechanisms of stabilization of Cd by biochar for agricultural soils.

Effects of emerging contaminants and heavy metals on variation in bacterial communities in estuarine sediments

Emerging contaminants (ECs) and heavy metals (HMs) are universally present together in estuarine sediments; despite this, their effects on microbial communities have been widely studied separately, rather than in consort. In this study, the combined effects of ECs and HMs on microbial communities were investigated in sediments from 11 major river estuaries around the Bohai Sea, China. Proteobacteria, Bacteroidetes, and Firmicutes were the dominant phyla in the sediments. Using Shannon indices, total phosphorus and total organic carbon were shown to affect microbial community structure. Redundancy analysis of microbial variation implicated Cd and As as the greatest pollutants, followed by Mn, Fe, Zn and Cu; no impacts from galaxolide (HHCB) and tonalide (AHTN) were found. Correlation analysis demonstrated that the concentration of ECs increased the abundance of certain bacteria (e.g., Haliangium, Altererythrobacter, Gaiella and Erythrobacter), and therefore these can be used as potential contamination indicators. Shannon indices and Chao1 indices showed that there were differences in the richness and diversity of bacterial communities in the sediments of 11 rivers. The principal coordinate analysis displayed higher similarity of bacterial community composition in estuarine sediments in Liaoning province than other regions. The results can be used to predict changes in estuary ecosystems to maintain their ecological balance and health.

Effects of Temperature and Nitrogen Application on Carbon and Nitrogen Accumulation and Bacterial Community Composition in Apple Rhizosphere Soil.

Malus sieversii grows on the slopes of the Tianshan Mountains in Xinjiang where the difference in daily temperature is significant. In recent years, the rhizosphere soil health of Malus sieversii has been severely impacted by anthropogenic disturbance and pathogenic infestation. The soil nutrient content and soil microorganism diversity are the main components of soil health. Low temperature has negative effects on soil bacterial community structure by inhibiting the accumulation of carbon and nitrogen. However, the effects of temperature and nitrogen application on soil carbon and nitrogen accumulation and the bacterial community composition in the rhizosphere soil of Malus sieversii are unclear. We set two temperature levels, i.e., low temperature (L) and room temperature (R), combined with no nitrogen (N0) and nitrogen application (N1) to explore the response of plant carbon and nitrogen uptake, rhizosphere soil carbon and nitrogen accumulation and bacterial community composition to temperature and nitrogen fertilization. At the same temperature level, plant 13C abundance (P-Atom13C), plant 15N absolute abundance (P-Con15N), soil 15N abundance (S-Atom15N) and soil urease, protease and glutaminase activities were significantly higher under nitrogen application compared with the no-nitrogen application treatment. The bacterial community diversity and richness indices of the apple rhizosphere soil in the N1 treatment were higher than those in the N0 treatment. The relative abundances of Actinobacteria, Rhodopseudomonas, and Bradyrhizobium were higher in the LN1 treatment than in the LN0 treatment. Redundancy analysis (RDA) showed that plant 13C absolute abundance (P-Con13C) and plant 15N absolute abundance (P-Con15N) were the main factors affecting the soil bacterial community composition. In summary, Nitrogen application can alleviate the effects of low temperature stress on the soil bacterial community and is of benefit for the uptakes of carbon and nitrogen in Malus sieversii plants.

Effects of Imazethapyr on Soybean Root Growth and Soil Microbial Communities in Sloped Fields

The herbicide imazethapyr was previously recommended for controlling weeds in soybean fields. However, the effects of imazethapyr on soil microbial communities and their relationship with crop root growth in sloped soils remain unclear. In this study, a field experiment was conducted on a sloped field to explore the effects of imazethapyr on crop root growth, microbial communities, microbial co-occurrence networks, and the interactions between microbes and crop root growth. The field experiment included two factors: slope and imazethapyr. The slope factor included three different slope gradients: 5° (S1), 10° (S2), and 15° (S3). The imazethapyr factor included two treatments: with (I1) and without (I0) imazethapyr. Thus, six total combinations of slope and imazethapyr treatments were tested in this study: S1I1, S2I1, S3I1, S1I0, S2I0, and S3I0. The results show that, compared to the I0 treatments, the I1 treatments significantly increased the soybean root length, surface area, and volume by 11.7~26.5 m, 171.7~324.2 cm2, and 1.8~3.1 cm3, respectively, across all the slopes. The Proteobacteria, Actinobacteriota, and Bacteroidota bacterial phyla and Ascomycota and Basidiomycota fungal phyla were found to be the top phyla represented bacterial and fungal communities. These five phyla were scattered in co-occurrence networks of bacterial and fungal communities, suggesting these phyla play critical roles in enhancing the stability of co-occurrence networks. Compared to the I0 treatments, the I1 treatments increased nodes from Proteobacteria, Actinobacteriota, and Bacteroidota phyla by 6.4%, 9.1%, and 11.2%, respectively, in the bacterial co-occurrence network. Similarly, in the fungal co-occurrence network, the I1 treatments improved nodes from Ascomycota and Basidiomycota phyla by 1.8% and 5.8%, respectively. Compared to the I0 treatments, the I1 treatments increased positive relations by 8.3% and 3.2%, respectively, in the bacterial and fungal co-occurrence networks. Moreover, the I1 treatments increased the relative abundance of root-promoting biomarkers and suppressed root-limiting biomarkers. However, the application of imazethapyr reduced the diversity and richness of bacterial and fungal communities in general. Furthermore, the nodes and links of bacterial co-occurrence networks in the I0 treatments were 9.2% and 78.8% higher than these in the I1 treatments. Similarly, the I1 treatments also decreased 17.9% of fungal community links compared to the I0 treatments. Our data also show that compared to the I0 treatments, the I1 treatments decreased almost all gene families encoding nitrogen and carbon cycling pathways. In conclusion, the application of imazethapyr increased soybean root growth by increasing root-promoting biomarkers and improved the stability and cooperation of co-occurrence networks of bacterial and fungal communities. However, the application of imazethapyr had some negative impacts on microbial communities, such as reducing the diversity of bacterial and fungal communities and nitrogen and carbon cycling pathways.

Influence of Alfalfa (Medicago sativa L.) at Various Growing Years on the Physico-chemical Properties and Microbiology of Irrigated Desert Soils

Background: The arid area of northwest China is the main producing area of alfalfa (Medicago sativa L.) characterized by low rainfall, low vegetation coverage and vulnerable ecosystem. However, there are still very few reports about the influence of alfalfa at various growing years on the physico-chemical properties and microbial community structure in typical northwestern irrigated desert soil. This study has important theoretical and practical guiding significance for providing reference and scientific evidence for local alfalfa industry development and protection of soil ecosystem to maintain efficient alfalfa production. Methods: The rhizosphere soils of “Sanditi” alfalfa and Longdong” alfalfa were collected to assess the influence of alfalfa varieties, growing years and growth stages on the physico-chemical properties, microbial biomass and microbial community structure. There were four treatments in this experiment: 1. “Sanditi” alfalfa planted in 2015 (S1); 2. “Sanditi” alfalfa planted in 2016 (S2); 3. “Sanditi” alfalfa planted in 2017 (S3); 4. “Longdong” alfalfa planted in 2017 (LD). Result: Soil of all treatments had consistent pH at 8.11-8.45. The average soil organic matter content was 11.02 g. kg-1, 11.43 g. kg-1, 11.26 g. kg-1 and 11.20 g. kg-1 respectively for LD, S1, S2 and S3 (P greater than 0.05). The total nitrogen content was 0.451 g. kg-1, 0.468 g. kg-1, 0.437 g. kg-1 and 0.428 g. kg-1, respectively for growing seasons of LD, S1, S2 and S3 (P greater than 0.05). The results suggested that alfalfa cropping did not significantly influence the soil organic matter content in 3 years. S1 significantly changed the ratio of fungal to bacterial typical fatty acids, which was significantly higher than S3 and LD, but insignificantly higher than S2. Continuous cropping of alfalfa in arid area affected the diversity of the fungi community and reduced soil bacterial community richness and diversity.

Straw Return and Nitrogen Fertilization to Maize Regulate Soil Properties, Microbial Community, and Enzyme Activities Under a Dual Cropping System.

Soil sustainability is based on soil microbial communities’ abundance and composition. Straw returning (SR) and nitrogen (N) fertilization influence soil fertility, enzyme activities, and the soil microbial community and structure. However, it remains unclear due to heterogeneous composition and varying decomposition rates of added straw. Therefore, the current study aimed to determine the effect of SR and N fertilizer application on soil organic carbon (SOC), total nitrogen (TN), urease (S-UE) activity, sucrase (S-SC) activity, cellulose (S-CL) activity, and bacterial, fungal, and nematode community composition from March to December 2020 at Guangxi University, China. Treatments included two planting patterns, that is, SR and traditional planting (TP) and six N fertilizer with 0, 100, 150, 200, 250, and 300 kg N ha–1. Straw returning significantly increased soil fertility, enzymatic activities, community diversity, and composition of bacterial and fungal communities compared to TP. Nitrogen fertilizer application increased soil fertility and enzymes and decreased the richness of bacterial and fungal communities. In SR added plots, the dominated bacterial phyla were Proteobacteria, Acidobacterioia, Nitrospirae, Chloroflexi, and Actinobacteriota; whereas fungal phyla were Ascomycota and Mortierellomycota and nematode genera were Pratylenchus and Acrobeloides. Co-occurrence network and redundancy analysis (RDA) showed that TN, SOC, and S-SC were closely correlated with bacterial community composition. It was concluded that the continuous SR and N fertilizer improved soil fertility and improved soil bacterial, fungal, and nematode community composition.

Evaluating the remediation potential of MgFe2O4-montmorillonite and its co-application with biochar on heavy metal-contaminated soils

In this work, a novel and efficient magnesium ferrite-modified montmorillonite (MgFe2O4-MMT) compound was prepared. MgFe2O4-MMT and biochar were mixed at 0:10, 1:9, 3:7, 4:6, and 10:0 w/w combinations and were used for heavy metal immobilization in soil polluted with multiple heavy metals. MgFe2O4-MMT can significantly increase soil alkalinity, and it exhibited the most optimal effect in immobilization of heavy metals in soil. The amounts of Cd, Pb, Cu, and Zn that were extracted by the toxicity characteristic leaching procedure (TCLP) decreased by 58.4%, 50.3%, 42.9%, and 24.7%, respectively. MgFe2O4-MMT can immobilize heavy metals through electrostatic interactions and cation exchange processes. Although, the immobilization of potentially toxic elements by MgFe2O4-MMT and biochar was inferior to that by MgFe2O4-MMT. The combined application of MgFe2O4-MMT and biochar dramatically increased the diversity and richness of the soil bacterial community. The Chao1 index for M3B7 treatment group was 1.7 and 1.2 times higher than that for the control and MgFe2O4-MMT treatment groups, respectively. The combination of biochar and MgFe2O4-MMT might be a cost-effective and ecological remediation approach for mild Pb and Cd contamination.

The carbon and nitrogen stoichiometry in litter-soil-microbe continuum rather than plant diversity primarily shapes the changes in bacterial communities along a tropical forest restoration chronosequence

Soil bacteria play core roles in mediating the functional linkage between above- and belowground components during forest restoration. However, the pattern and mechanism through which plants and soils influence bacterial communities remain unclear. This study aimed to quantify the contributions of plant community and soil characteristics to shifts in bacterial composition and diversity along a tropical forest restoration chronosequence in the Xishuangbanna. We found a negative effect of forest restoration on bacterial composition and a positive impact on the diversity. Forest restoration changed bacterial communities from being oligotrophic Acidobacteria and Actinobacteria dominatedto copiotrophic Proteobacteria and Firmicutes dominated. Forest restoration also induced a 1.5–1.6 fold increase in OTU richness and diversity of bacterial communities. Soil variables, including plant litter, contributed 46.3–58.1% to the variations in bacterial composition and diversity, while the contribution of plant community was 6.4–13.8%. Furthermore, the increase in plant richness and diversity had minor contribution to variations in bacterial diversity and composition during forest restoration. Soil bacterial diversity was primarily explained by the elevated levels of carbon and nitrogen stoichiometry in the litter-soil-microbe continuum, but litter was explained by the increased plant diversity. In contrast, soil bacterial composition was negatively correlated with biomass, nitrogen, and carbon:nitrogen of the litter, as well as the level of soil carbon and nitrogen pools. Our data suggested that the carbon and nitrogen stoichiometry in litter-soil-microbe continuum rather than plant diversity primarily shaped the changes in bacterial composition and diversity along tropical forest restoration.

Influence of Agricultural Practices on Bacterial Community of Cultivated Soils

Bacterial communities play an important role in maintaining stable functioning of soil ecosystems, participating in decomposition of plant residues, accumulation of organic matter, formation of soil aggregates and in the cycle of nutrients. For agroecosystems, maintaining the diversity of microbiocenosis is especially critical because they are essentially less stable and are dependent on external control. The agricultural practices used today (plowing, application of synthetic fertilizers) can negatively affect the richness and diversity of the soil bacterial communities. The solution to this problem may be the application of alternative farming methods to preserve the structural and functional richness of soil (reduced tillage, conservation tillage, no tillage, organic farming). Data on composition and diversity of soil microbiocenosis are important for further forecasting the impact of agriculture and development of effective methods on preserving and increasing soil fertility. This review presents the results of recent studies on the impact of agriculture on the soil bacterial communities. Attention is mainly paid to the effects of applying inorganic and organic fertilizers on the structure and diversity of soil microbiocenosis; the influence of the farming system (different methods of soil cultivation, organic and traditional systems); the influence of cover crops and crop rotation on the microbial community of agricultural soils.

English

Mulching has been used widely to improve the production capacity of the soil, yield and the quality of wine grapes (Vitis vinifera L. cv. Cabernet Sauvignon). However, the ecological mechanisms underlying the mulching materials were not well understood. This study aimed to evaluate the effects of different mulching materials on soil chemical properties, bacterial community and wine grape quality. Experiments were performed at a grape-yard on the six-year-old wine grape ‘Vitis vinifera L. cv. Cabernet sauvignon. Five kinds of mulching materials include living turfgrass (Grass), living Herba portulacae (Por), inorganic plastic black film (Film), organic chips of wood (Wood), and grape branches (Branch) were applied, while clean tillage (CK) was treated as a control. Soil chemical properties and grape quality indicators were measured. Soil bacterial community diversity was detected using the Illumina Miseq sequencing for the 16S rRNA gene V3-V4 region. Mulching with plastic film, wood chips and Herba portulacae (Por) increased the content of soil organic matter, available N, P and K, total N and P. Film, grass, branch and Por mulching materials improved the content of tannin, anthocyanin, total phenol and titratable acid in grape (p&lt;0.05). Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria and Gemmatimonadetes were abundant bacteria. Mulching with grape branch and portulacae increased the relative abundance of Gemmatimonadetes and Chloroflexi phylum, Gemmatimonadaceae family, and decreased Micrococcaceae family and Pseudarthrobacter genus. Mulching with living, organic, or inorganic changed chemical properties and grape quality indicators. These changes might be correlated with the altered soil bacterial community diversity and richness. © 2022 Friends Science Publishers

Combined Bioremediation of Bensulfuron-Methyl Contaminated Soils With Arbuscular Mycorrhizal Fungus and Hansschlegelia zhihuaiae S113.

Over the past decades, because of large-scale bensulfuron-methyl (BSM) application, environmental residues of BSM have massively increased, causing severe toxicity in rotation-sensitive crops. The removal of BSM from the environment has become essential. In this study, the combined bioremediation of the arbuscular mycorrhizal fungi (AMF) Rhizophagus intraradices and BSM-degrading strain Hansschlegelia zhihuaiae S113 of BSM-polluted soil was investigated. BSM degradation by S113 in the maize rhizosphere could better promote AMF infection in the roots of maize, achieving an infection rate of 86.70% on the 36th day in the AMF + S113 + BSM group. Similarly, AMF enhanced the colonization and survival of S113 in maize rhizosphere, contributing 4.65 × 105 cells/g soil on the 15th day and 3.78 × 104 cells/g soil on the 20th day to a population of colonized-S113 (based possibly on the strong root system established by promoting plant-growth AMF). Both S113 and AMF coexisted in rhizosphere soil. The BSM-degrading strain S113 could completely remove BSM at 3 mg/kg from the maize rhizosphere soil within 12 days. AMF also promoted the growth of maize seedlings. When planted in BSM-contaminated soil, maize roots had a fresh weight of 2.59 ± 0.26 g in group S113 + AMF, 2.54 ± 0.20 g in group S113 + AMF + BSM, 2.02 ± 0.16 g in group S113 + BSM, and 2.61 ± 0.25 g in the AMF group, all of which exceeded weights of the control group on the 36th day except for the S113 + BSM group. Additionally, high-throughput sequencing results indicated that simultaneous inoculation with AMF and strain S113 of BSM-polluted maize root-soil almost left the indigenous bacterial community diversity and richness in maize rhizosphere soil unaltered. This represents a major advantage of bioremediation approaches resulting from the existing vital interactions among local microorganisms and plants in the soil. These findings may provide theoretical guidance for utilizing novel joint-bioremediation technologies, and constitute an important contribution to environmental pollution bioremediation while simultaneously ensuring crop safety and yield.

Characteristics of Bacterial and Archaeal Communities in Microbial‐Enhanced Constructed Wetlands under NaCl Stress

AbstractHigh salt concentrations can restrict or inhibit microorganism activity, which can detrimentally influence pollutant degradation. In this study, intertidal wetland sediments (IWS) are introduced into constructed wetlands (CWs) as sources of microorganisms. The richness and evenness of bacterial and archaeal microbial communities in the presence of 150 × 10−3 m NaCl are evaluated by high‐throughput sequencing. The distinction of dominant functional microorganisms in CWs with and without IWS is also analyzed. Anaerolineales and thermomicrobia are the dominant microorganisms in IWS–CWs in the saline condition and are related to methane production. The abundance of Alphaproteobacteria, Myxococcales, and Xanthomonadales, related to dehydrogenation, is relatively high in IWS–CWs. The addition of IWS induces further production of Anaerolineaceae and Geobacteraceae, which is positively correlated with the phosphorus‐accumulating and sulfate‐reducing stages. The dominant archaea phyla in IWS–CWs in the saline condition are Thaumarchaeota (87.5%) and Euryarchaeota (12.2%), which are involved in ammonia‐oxidizing and methane‐producing processes, respectively. These functional microbial communities are beneficial to the degradation and transformation of pollutants in the CWs. Thus, IWS with various halophilic and pollutant‐degrading microorganisms can be considered effective microbial sources to enhance the pollutant removal abilities of CWs.

ATP catabolism and bacterial succession in postmortem tissues of mud crab (Scylla paramamosain) and their roles in freshness

The seafood microbiome is highly diverse and plays an essential role in the spoilage of seafood. Nevertheless, how such a diverse microbiome influences freshness of mud crab (Scylla paramamosain) remains unclear. Here we investigated the postmortem ATP catabolism and succession of the bacterial community in the hepatopancreas and muscle of S. paramamosain using a high-performance liquid chromatography method and 16S rRNA gene amplicon sequencing. Our results showed a tissue-dependent change in ATP catabolism determinized the differences in the changes of nucleotide freshness indices of hepatopancreas and muscle over postmortem time of mud crab. The muscle K value could be used as an optimal nucleotide freshness indicator for the freshness of mud crab, with a proposed threshold of 20%. From a microbiota perspective, a more significant bacterial community change was observed in the muscle than in the hepatopancreas. These changes could result in a close relationship between ATP and its catabolites and microbial taxa in the muscle. Moreover, Photobacterium, Peptostreptococcaceae, average path distance, OTU richness, and Shannon index of muscle bacterial community markedly contributed to K value. These findings suggest that the mud crab of 4 h postmortem at room temperature is still edible. Notably, the importance of microbial community composition and interaction for the spoilage of mud crab should be carefully considered.

Properties of sediment dissolved organic matter respond to eutrophication and interact with bacterial communities in a plateau lake

Sediment dissolved organic matter (DOM) in inland waters is commonly affected by environmental changes. However, knowledge about how sediment DOM responds to eutrophication and the associations between sediment DOM and bacterial communities requires further investigation. We selected a sediment core from Dianchi Lake (China) that was dated from 1864 to 2019 by the activity of radionuclides (210Pb and 137Cs). δ13CDOC changes fit well with the historical record that heavy eutrophic status in Dianchi Lake were observed since 1980s. Large amounts of dissolved organic carbon (DOC), chromophoric (CDOM) and fluorescent (FDOM) DOM accumulated at the top of the sediments during the eutrophication period (1982-present). The additional algae sources with a higher degradation rate altered the composition, aromaticity and humification of DOM. After long-term mineralization, the remaining DOM became more and more recalcitrant and kept a relatively stable level at older sediments. A co-occurrence network analysis revealed that Proteobacteria, Chloroflexi, Acidobacteriota, Bacteroidota and Desulfobacterota were the most abundant species at the phylum level and clustered into three primary modules. Different microbes shared unique preferences for niches, causing a heterogeneous bacterial distribution at different depths. We conducted Spearman's correlation and redundancy analysis (RDA) to explore potential interactions between bacterial community and sediment DOM. The richness and diversity of bacterial communities were positively related to DOM content, suggesting abundant DOM can produce more available resources for bacteria. RDA results showed some specific species might modify DOM composition and structure. This study suggests that sediment DOM properties were regulated by source transformation during eutrophication, and emphasizes the importance of microbial role on sediment biogeochemical process.

Dissolved organic carbon, an indicator of soil bacterial succession in restored wetland under freeze-thaw cycle

The moisture availability is of great significance to the physical, chemical and biological processes of soil, however, information regarding how freeze-thaw cycles (FTCs) affect the bacterial community of soil with different moisture contents is limited. In this work, we studied the relationship between FTCs and soil bacterial community under different moisture content (field capacity, FC and saturated moisture content, SMC). The results showed that FTCs decreased the richness and diversity of the soil bacterial community. Bacteria diversity were significantly decreased after the second FTC (FTC2). Thereafter, bacterial diversity with a saturated moisture content returned to the pre-freeze-thaw level, but the recovery of bacterial diversity in soil with the field capacity was lower than that of the saturated moisture content. Frequent FTCs accelerate the turnover of dissolved organic carbon DOC by affecting the carbon metabolism of microbial communities. Adjusting moisture to SMC can increase the stability of carbon. Our results provided reference to for the management of restored wetland.

Constructing Micro-Landscapes: Management and Selection Practices on Microbial Communities in a Traditional Fermented Beverage

Colonche is a traditional beverage produced in Mexico by the fermentation of fruits of several cacti species. In the Meridional Central Plateau region of Mexico, where this study was conducted, it is mainly produced with fruits of Opuntia streptacantha; there, the producers perform spontaneous fermentation and/or fermentations through inoculums. Several factors can change the microbial community structure and dynamics through the fermentation process, but little attention has been directed to evaluate what type and extent of change the human practices have over the microbial communities. This study aims to assess the microbiota under spontaneous and inoculated fermentation techniques, the microorganisms present in the inoculums and containers, and the changes of microbiota during the process of producing colonche with different techniques. We used next-generation sequencing of the V3-V4 regions of the 16S rRNA gene and the ITS2, to characterize bacterial and fungal diversity associated with the different fermentation techniques. We identified 701 bacterial and 203 fungal amplicon sequence variants (ASVs) belonging to 173 bacterial and 187 fungal genera. The alpha and beta diversity analysis confirmed that both types of fermentation practices displayed differences in richness, diversity, and community structure. Richness of bacteria in spontaneous fermentation (0D = 136 ± 0.433) was higher than in the inoculated samples (0D = 128 ± 0.929), while fungal richness in the inoculated samples (0D = 32 ± 0.539) was higher than in spontaneous samples (0D = 19 ± 0.917). We identified bacterial groups like Lactobacillus, Leuconostoc, Pediococcus and the Saccharomyces yeast shared in ferments managed with different practices; these organisms are commonly related to the quality of the fermentation process. We identified that clay pots, where spontaneous fermentation is carried out, have an outstanding diversity of fungal and bacterial richness involved in fermentation, being valuable reservoirs of microorganisms for future fermentations. The inoculums displayed the lowest richness and diversity of bacterial and fungal communities suggesting unconscious selection on specific microbial consortia. The beta diversity analysis identified an overlap in microbial communities for both types of fermentation practices, which might reflect a shared composition of microorganisms occurring in the Opuntia streptacantha substrate. The variation in the spontaneous bacterial community is consistent with alpha diversity data, while fungal communities showed less differences among treatments, probably due to the high abundance and dominance of Saccharomyces. This information illustrates how traditional management guides selection and may drive changes in the microbial consortia to produce unique fermented beverages through specific fermentation practices. Although further studies are needed to analyze more specifically the advantages of each fermentation type over the quality of the product, our current analysis supports the role of traditional knowledge driving it and the relevance of plans for its conservation.

Exploring of seasonal dynamics of microbial community in multispecies fermentation of Shanxi mature vinegar

The constituents of fermentation foods vary seasonally and the microbiota plays a crucial role in metabolites formation. Here, the diversity and succession of microbiota of Shanxi mature vinegar produced with solid-solid fermentation craft have been investigated by Illumina Hiseq sequencing in both summer and winter. Obvious differences were observed in the structure of microbiota between summer and winter, and the bacterial community showed a significant difference (P < 0.05). Alpha diversity analysis showed that the diversity and richness of bacterial community were basically higher than that of fungal community in both summer and winter. For bacterial community, Lactobacillus and Limosilactobacillus were the two major group bacteria in the fermentation process of Shanxi mature vinegar in summer, and they dominated in acetic acid fermentation and alcoholic fermentation stages, respectively. Lactobacillus and Acetobacter were the two major group bacteria during the fermentation of Shanxi mature vinegar in winter. Saccharomyces, Saccharomycopsis, and Issatchenkia were the main yeasts in both seasons, while the dominant mould was Rhizopus in summer and Monascus in winter, respectively. The diversity of yeasts and moulds in winter was far greater than that in summer, especially in alcoholic fermentation stage. Collectively, our work revealed critical insights into effect of seasonal variation on the structure of microbiota of Shanxi mature vinegar, and was relevant in understanding the relationships between environmental change and microbiota.