Changes In Bacterial Community Composition Research Articles

Effects of the Long-Term Continuous Cropping of Yongfeng Yam on the Bacterial Community and Function in the Rhizospheric Soil

Replant disease caused by continuous cropping commonly occurs in yam with consecutive monoculture. However, little is known about how the continuous cropping of yam affects the rhizospheric soil bacterial community structure. In this study, the effects of continuous cropping on rhizospheric soil characteristics, bacterial diversity, and community structure were investigated in the Yongfeng yam fields under monoculture for 1, 5, 10, 15, and 20 years. Long-term monoculture caused soil acidification and increased the concentration of available potassium (AK) and available phosphorus (AP), and soil bacterial richness, but decreased the soil bacterial diversity. An exception was for the field under monoculture for 20 years as it showed the highest bacterial diversity. The relative abundance of beneficial bacteria, such as Proteobacteria, Actinobacteria, and Chloroflexi decreased while the relative abundance of harmful bacteria, including Gemmatimonadetes and Acidobacteria, increased with an extended continuous cultivation time. The networks varied among yams with different cultivation years and became complex with the increase in cultivation years. However, after time in monoculture, the bacterial network decreased gradually and existed stably. These changes in bacterial community composition and co-occurrence of networks may increase the potential risk of soil-borne disease and reduce the yield and quality of Yongfeng yam.

Responses of Free-Living Planktonic Bacterial Communities to Experimental Acidification and Warming

Climate change driven by human activities encompasses the increase in atmospheric CO2 concentration and sea-surface temperature. Little is known regarding the synergistic effects of these phenomena on bacterial communities in oligotrophic marine ecosystems that are expected to be particularly vulnerable. Here, we studied bacterial community composition changes based on 16S rRNA sequencing at two fractions (0.1-0.2 and >0.2 μm) during a 10- day fully factorial mesocosm experiment in the eastern Mediterranean where the pH decreased by ~0.3 units and temperature increased by ~3 °C to project possible future changes in surface waters. The bacterial community experienced significant taxonomic differences driven by the combined effect of time and treatment; a community shift one day after the manipulations was noticed, followed by a similar state between all mesocosms at the third day, and mild shifts later on, which were remarkable mainly under sole acidification. The abundance of Synechococcus increased in response to warming, while the SAR11 clade immediately benefited from the combined acidification and warming. The effect of the acidification itself had a more persistent impact on community composition. This study highlights the importance of studying climate change consequences on ecosystem functioning both separately and simultaneously, considering the ambient environmental parameters.

Temperature fluctuation promotes the thermal adaptation of soil microbial respiration.

The magnitude of the feedback between soil microbial respiration and increased mean temperature may decrease (a process called thermal adaptation) or increase over time, and accurately representing this feedback in models improves predictions of soil carbon loss rates. However, climate change entails changes not only in mean temperature but also in temperature fluctuation, and how this fluctuation regulates the thermal response of microbial respiration has never been systematically evaluated. By analysing subtropical forest soils from a 2,000 km transect across China, we showed that although a positive relationship between soil microbial biomass-specific respiration and temperature was observed under increased constant incubation temperature, an increasing temperature fluctuation had a stronger negative effect. Our results further indicated that changes in bacterial community composition and reduced activities of carbon degradation enzymes promoted the effect of temperature fluctuation. This adaptive response of soil microbial respiration suggests that climate warming may have a lesser exacerbating effect on atmospheric CO2 concentrations than predicted.

尖峰岭热带天然林不同土层细菌群落多样性和组成的海拔变异规律

PDF HTML阅读 XML下载 导出引用 引用提醒 尖峰岭热带天然林不同土层细菌群落多样性和组成的海拔变异规律 DOI: 10.5846/stxb202203090570 作者: 作者单位: 作者简介: 通讯作者: 中图分类号: 基金项目: 国家自然科学基金项目（32171643，U1703332） The altitudinal patterns of bacterial community diversity and composition at different soil depths in Jianfengling mountain tropical forest Author: Affiliation: Fund Project: The National Natural Science Foundation of China (General Program, Key Program, Major Research Plan) 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:土壤微生物群落结构沿海拔梯度的变异是微生物生物地理学分异和群落空间分布的重要内容，然而，热带森林土壤微生物多样性及其群落特征的海拔模式尚不明确。研究海南省尖峰岭自然保护区0-20cm和20-40cm土壤细菌多样性和群落组成沿海拔梯度（400-1410m）的变化及其与环境因子的关系。结果表明：在0-20cm土壤微生物生物量碳、生物量氮和生物量磷随海拔升高（峰顶降低）而增加，20-40cm土壤微生物生物量碳、生物量氮和生物量磷随海拔升高呈先升高后降低趋势；整体上，变形菌门、放线菌门、酸杆菌门、拟杆菌门、厚壁菌门在0-20cm中占优势，丰度总和占该层细菌总量的88.17%；变形菌门、放线菌门、酸杆菌门、厚壁菌门、绿弯菌门在20-40cm中占优势，丰度总和占该层细菌总量的90.82%；随海拔增加，0-20cm细菌多样性线性减少，20-40cm细菌多样性变化不显著；沿海拔梯度，0-20cm细菌群落组成可分为低（409-1018m），中（1018-1357m）和高（1410m）三个海拔聚集群落，20-40cm细菌群落组成随海拔无显著性变化；两土层细菌多样性与土壤pH显著正相关，土壤细菌群落组成在0-20cm主要受年均温度和pH影响，20-40cm受年均温度和土壤有机碳影响；根据Bray-Curtis指数，0-20cm和20-40cm土壤细菌相似性随地理距离的增加逐渐降低，细菌群落相似性随环境距离的增大也逐渐降低。总之，尖峰岭土壤细菌多样性和群落组成的海拔格局受土壤深度影响，且驱动细菌群落组成变化的因素在土层间不同，暗示在未来气候变化背景下，热带森林0-20cm和20-40cm土壤微生物群落可能具有不同的响应机制。 Abstract:The variation of soil microbial community structure along the altitudinal gradient is an important content of microbial biogeographic differentiation and community spatial distribution. However, the altitudinal pattern of soil microbial diversity and its community characteristics in tropical forests is not clear. This paper studied the changes of bacterial diversity and community composition and their relationship with environmental factors in 0-20cm and 20-40cm soil depths along the altitudinal gradient (400-1410 m) in Jianfengling Nature Reserve, Hainan Province. The results showed that the soil microbial biomass carbon, biomass nitrogen and biomass phosphorus increased with the elevation of 0-20cm (the peak decreased), and the soil microbial biomass carbon, biomass nitrogen and biomass phosphorus increased first and then decreased with the elevation of 20-40cm. On the whole, Proteobacteria, Actinomycetes, Acidobacteria, Bacteroidetes and Firmicutes are dominant in 0-20cm, and the total abundance accounts for 88.17% of the total bacteria in this layer; Proteobacteria, Actinomycetes, Acidobacteria, Firmicutes and Chloroflexi are dominant in 20-40cm, and the total abundance accounts for 90.82% of the total bacteria in this layer. With the increase of altitude, the bacterial diversity decreased linearly in 0-20cm, and that of 20-40cm did not change significantly. The bacterial community composition of 0-20cm can be divided into three communities at low altitude (409-1018 m), medium altitude (1018-1357 m), and high altitude (1410 m) and the bacterial community composition of 20-40cm has no significant change with altitude. There was a significantly positive correlation between bacterial diversity and soil pH in the two soil depths. The composition of soil bacterial community was mainly affected by mean annual temperature and pH at 0-20cm, and by mean annual temperature and soil organic carbon at 20-40cm. According to the Bray Curtis index, the similarity of bacteria in 0-20cm and 20-40cm soil depths decreased with the increase of geographical distance, and the similarity of bacterial community also decreased with the increase of environmental distance. In a word, the altitudinal pattern of soil bacterial diversity and community composition in Jianfengling is affected by soil depth, and the factors driving the change of bacterial community composition are different among soil depths. It is suggested that the soil microbial communities in 0-20cm and 20-40cm of tropical forests may have different response mechanisms under the background of future climate change. 参考文献 相似文献 引证文献

Crawfish shell- and Chinese banyan branch-derived biochars reduced phytoavailability of As and Pb and altered community composition of bacteria in a contaminated arable soil

Globally, soil contamination with arsenic (As) and lead (Pb) has become a severe environmental issue. Herein, a pot experiment was conducted using pak choi (Brassica chinensis L.) to investigate the effects of biochars derived from crawfish (Procambarus clarkia) shells (CSB) and Chinese banyan (Ficus microcarpa) branches (CBB) on the phytoavailability of As and Pb, and bacterial community composition in soils. Our results showed that the application of CSB and CBB decreased the concentrations of DTPA-extractable Pb in soils ranging from 26.8 % to 28.8 %, whereas CSB increased the concentration of NH4H2PO4-extractable As in soils, compared to the control. Application of both biochars reduced the uptake of As and Pb in the edible part of pak choi. In addition, application of CBB significantly (P < 0.05) increased the activities of α-glucosidase, β-glucosidase, cellobiohydrolase, and acid phosphomonoesterase by 55.0 %, 54.4 %, 195.1 %, and 76.7 %, respectively, compared to the control. High-throughput sequencing analysis revealed that the predominant bacteria at the phyla level in both biochar-treated soils were Firmicutes, Proteobacteria, and Actinobacteriota. Redundancy and correlation analyses showed that the changes in bacterial community composition could be related to soil organic carbon content, As availability, and nutrient availability in soils. Overall, the Chinese banyan branch biochar was more suitable than the crawfish shell biochar as a potential amendment for the remediation of soils co-contaminated with As and Pb.

Brassica seed meal fumigation restores beneficial bacterial communities by enriching taxa with high resistance and resilience

PurposeBrassica seed meals (BSMs) are widely used as biofumigants to control various soil-borne plant diseases. However, the mechanism of bacterial community reconstruction following fumigation with BSMs remains poorly understood.MethodsIn the present study, to decipher the mechanism of bacterial community reconstruction in fumigated soil and to understand the effect of bacterial communities in fumigated soil on rhizosphere recruitment and subsequent disease control, we investigated the bulk soil and rhizosphere bacterial communities using field experiments in soils treated with various fumigants (Brassica campestris seed meal, Brassica juncea seed meal, and the chemical fumigant dazomet) in two greenhouses subsequently used to grow tomato and cantaloupe, respectively.ResultsThis study revealed that bulk soil bacterial community composition changed significantly after fumigation extinction and recovery. Firmicutes and Proteobacteria, showing high resistance and resilience in the extinction and recovery processes, respectively, represented the key microorganisms for community reconstruction and rhizosphere recruitment. Moreover, nutrients supplied by BSMs, especially available phosphorus (AP), in fumigated soils determined the post-restoration changes in bacterial community composition. Additionally, BSMs showed greater potential than chemical fumigant dazomet in rebuilding beneficial bacterial communities and controlling potential soil pathogens by enriching gram-positive phyla Firmicutes and Actinobacteria and their respective affiliated genera Bacillus and Streptomyces.ConclusionThese results provide a fundamental ecological understanding of the response of soil-inhabiting microbes to fumigation and the reconstruction of soil beneficial bacterial communities after BSM fumigation. Thus, this study improves the understanding of the effects of biofumigants on soil-borne plant disease control in agriculture.

Changes in Soil Microbial Communities under Mixed Organic and Inorganic Nitrogen Addition in Temperate Forests

Investigating the response of soil microbial communities to nitrogen (N) deposition is critical to understanding biogeochemical processes and the sustainable development of forests. However, whether and to what extent different forms of N deposition affect soil microbial communities in temperate forests is not fully clear. In this work, a field experiment with three years of simulated nitrogen deposition was conducted in temperate forests. The glycine and urea were chosen as organic nitrogen (ON) source, while NH4NO3 was chosen as inorganic nitrogen (IN) source. Different ratios of ON to IN (CK = 0:0, Mix-1 = 10:0, Mix-2 = 7:3, Mix-3 = 5:5, Mix-4 = 3:7, Mix-5 = 0:10) were mixed and then used with equal total amounts of 10 kg·N·ha−1·a−1. We determined soil microbial diversity and community composition for bacteria and fungi (16S rRNA and ITS), and soil parameters. Different forms of N addition significantly changed the soil bacterial and fungal communities. Mixed N sources had a positive effect on soil bacterial diversity and a negative effect on fungal diversity. Bacterial and fungal community structures were significantly separated under different forms of N addition. Soil pH was the main factor affecting the change in fungal community structure, while bacterial community structure was mainly controlled by STN. We also found that Proteobacteria, Acidobacteriota, Basidiomycota and Ascomycota were the most abundant phyla, regardless of the form of N addition. RDA showed that C/P and NH4+ were the main factors driving the change in bacterial community composition, and C/P, pH and C/N were the main factors driving the change in fungal community composition. Our results indicate that different components of N deposition need to be considered when studying the effects of N deposition on soil microorganisms in terrestrial ecosystems.

The Influence of Host Specificity and Temperature on Bacterial Communities Associated with Sargassum (Phaeophyceae) Species.

Host-related microbiota are critically important for the adaptation/acclimation of hosts to changing environments, but how environmental factors andhost characteristics shape the microbial communities remains largely unknown. We investigated the effects of temperature on habitat-forming macroalgae and their associated bacterial communities. Three Sargassum species (S. horneri, S.fusiforme, and S. thunbergii) and seawater samples were sampled in Gouqi Island, China, and these macroalgal samples were incubated at different temperatures (10, 20, and 27°C) for 7 d. Bacterial communities were identified from the 16S rRNA gene V3-V4 regions. The algae-associated bacterial communities of the field samples were significantly different from seawater, implying host specificity. During laboratory incubation, decreased physiological status (photosynthetic rate and oxidative stress response) was detected for all the species at 10°C, especially with regard to S. horneri and S. fusiforme. For each host, associated bacterial communities at 20 and 27°C clustered closely, and these were separated from samples at 10°C based on constrained PCoA analyses. Permutational multivariate analysis of variance revealed that algae-associated bacterial communities were more affected by host species (23.3%) than by temperature (2.48%) during laboratory incubation. The changes in bacterial community composition may be influenced by algae metabolites, which should be tested in a future study. These results further contribute to our understanding of algal microbiome changes in response to environmental changes.

Dynamics and prevalence of specific hydrocarbonoclastic bacterial population with respect to nutrient treatment levels in crude oil sludge.

The bacterial community composition in soil sediments changes with respect to nutrient concentrations and environmental conditions. Reports on the correlation between bacterial populations and inorganic nutrient concentrations in oily sediments are limited. The present time series study reports the prevalence of specific hydrocarbon-degrading bacterial communities in nutrient-treated oily sludge microcosms. The hydrocarbon degradation was maximum at 625µg nitrogen (N) and 62.5µg phosphorus (P)/g sludge sediment. The 16S rRNA gene-based DGGE analyses revealed noticeable changes in bacterial community composition with time and levels of nutrient treatment. BLASTn analysis of the 16S rRNA gene clone sequence showed the abundance of γ-Proteobacteria (44%), α-Proteobacteria (16%), β-Proteobacteria (10%), CFB (4%), and unidentified bacterial clones (26%). The catechol 1,2-dioxygenase (C12O) and catechol 2,3-dioxygenase (C23O) gene clones were affiliated to the genus Sphingomonas, highlighting the vital role of Sphingomonas in aromatic hydrocarbon degradation. The quantity of the 16S rRNA gene and the alkane hydroxylase (alkB) gene reached maximum levels in extended duration microcosms treated with 625µgN and 62.5µg P/g sludge sediment. In contrast, the C12O gene reached its highest abundance at a low N concentration.

Recovery trajectories of the bacterial community at distances in the receiving river under wastewater treatment plant discharge

Microbes in rivers are an important part of the biogeochemical cycle in aquatic ecosystems, and understanding the major factors that influence the composition of microbial communities has an important role in assessing and improving ecosystem functioning. A high-throughput 16 S rRNA gene sequencing technique was employed to sequence bacterial communities in 21 sediment samples and 21 water samples from an urban river WWTP (wastewater treatment plant) discharge. A systematic study of changes in bacterial community composition in downstream river sediment and water was conducted. The study found that compared with the bacterial diversity in the natural upstream area of the wastewater outfall, the bacterial diversity in the sediment lower reaches decreased significantly, while the bacterial abundance and diversity in the water increased significantly. The Mantel test and redundancy analysis showed that the downstream distance and physicochemical properties were significantly related to the succession of bacterial communities in the sediment downstream of the WWTP discharge. Among them, TOC (total organic carbon) was the most important factor affecting the change in the bacterial community in the downstream sediment. The physicochemical properties were significantly correlated with the succession of bacterial communities in the water downstream of the WWTP discharge. Among them, TN (total nitrogen), PO43--P (phosphorus phosphate) and TP (total phosphorus) were the main factors that affected the change in the bacterial community in the downstream water. Key taxa in the co-occurrence network at different distances downstream reflected the depth of the effect of the WWTP effluent on the bacterial community. The bacterial community in the lower reaches of the river sediment showed a strong recovery ability under the influence of pollutants, while the bacterial community in the lower reaches of the river water was difficult to recover under the influence of pollutants. In general, pollutants contained in effluent are the key to changing the composition of bacterial communities in the lower reaches of the river, but exogenous bacteria in effluent are not. This study provides a basis for further improving the effluent discharge standards of WWTPs in the future.

Reactive transport of micropollutants in laboratory aquifers undergoing transient exposure periods

Groundwater quality is of increasing concern due to the ubiquitous occurrence of micropollutant mixtures. Stream-groundwater interactions near agricultural and urban areas represent an important entry pathway of micropollutants into shallow aquifers. Here, we evaluated the biotransformation of a micropollutant mixture (i.e., caffeine, metformin, atrazine, terbutryn, S-metolachlor and metalaxyl) during lateral stream water flow to adjacent groundwater. We used an integrative approach combining concentrations and transformation products (TPs) of the micropollutants, compound-specific isotope analysis (δ13C and δ15N), sequencing of 16S rRNA gene amplicons and reactive transport modeling. Duplicate laboratory aquifers (160 cm × 80 cm × 7 cm) were fed with stream water and subjected over 140 d to three successive periods of micropollutant exposures as pulse-like (6000 μg L−1) and constant (600 μg L−1) injections under steady-state conditions. Atrazine, terbutryn, S-metolachlor and metalaxyl persisted in both aquifers during all periods (<10 % attenuation). Metformin attenuation (up to 14 %) was only observed from 90 d onwards, suggesting enhanced degradation over time. In contrast, caffeine dissipated during all injection periods (>90 %), agreeing with fast degradation rates (t1/2 < 3 d) in parallel microcosm experiments and detection of TPs (theobromine and xanthine). Significant stable carbon isotope fractionation (Δδ13C ≥ 6.6 ‰) was observed for caffeine in both aquifers, whereas no enrichment in 15N occurred. A concentration dependence of caffeine biotransformation in the aquifers was further suggested by model simulations following Michaelis-Menten kinetics. Changes in bacterial community composition reflected long-term bacterial adaptation to micropollutant exposures. Altogether, the use of an integrative approach can help to understand the interplay of subsurface hydrochemistry, bacterial adaptations and micropollutants biotransformation during stream-groundwater interactions.

Production of diverse brGDGTs by Acidobacterium Solibacter usitatus in response to temperature, pH, and O2 provides a culturing perspective on brGDGT proxies and biosynthesis.

Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are bacterial membrane lipids that are frequently employed as paleoenvironmental proxies because of the strong empirical correlations between their relative abundances and environmental temperature and pH. Despite the ubiquity of brGDGTs in modern and paleoenvironments, the source organisms of these enigmatic compounds have remained elusive, requiring paleoenvironmental applications to rely solely on observed environmental correlations. Previous laboratory and environmental studies have suggested that the globally abundant bacterial phylum of the Acidobacteria may be an important brGDGT producer in nature. Here, we report on experiments with a cultured Acidobacterium, Solibacter usitatus, that makes a large portion of its cellular membrane (24 ± 9% across all experiments) out of a structurally diverse set of tetraethers including the common brGDGTs Ia, IIa, IIIa, Ib, and IIb. Solibacter usitatus was grown across a range of conditions including temperatures from 15 to 30°C, pH from 5.0 to 6.5, and O2 from 1% to 21%, and demonstrated pronounced shifts in the degree of brGDGT methylation across these growth conditions. The temperature response in culture was in close agreement with trends observed in published environmental datasets, supporting a physiological basis for the empirical relationship between brGDGT methylation number and temperature. However, brGDGT methylation at lower temperatures (15 and 20°C) was modulated by culture pH with higher pH systematically increasing the degree of methylation. In contrast, pH had little effect on brGDGT cyclization, supporting the hypothesis that changes in bacterial community composition may underlie the link between cyclization number and pH observed in environmental samples. Oxygen concentration likewise affected brGDGT methylation highlighting the potential for this environmental parameter to impact paleotemperature reconstruction. Low O2 culture conditions further resulted in the production of uncommon brGDGT isomers that could be indicators of O2 limitation. Finally, the production of brGTGTs (trialkyl tetraethers) in addition to the previously discovered iso-C15-based mono- and diethers in S. usitatus suggests a potential biosynthetic pathway for brGDGTs that uses homologs of the archaeal tetraether synthase (Tes) enzyme for tetraether synthesis from diethers.

Dispersal of bacteria and stimulation of permafrost decomposition by Collembola

Abstract. Contrary to most soils, permafrost soils have the atypical feature of being almost entirely deprived of soil fauna. Abiotic constraints on the fate of permafrost carbon after thawing are increasingly understood, but biotic constraints remain scarcely investigated. Incubation studies, essential to estimate effects of permafrost thaw on carbon cycling, typically measure the consequences of permafrost thaw in isolation from the topsoil and thus do not account for the effects of altered biotic interactions because of e.g. colonization by soil fauna. Microarthropods facilitate the dispersal of microorganisms in soil, both on their cuticle (ectozoochory) and through their digestive tract (endozoochory), which may be particularly important in permafrost soils, considering that microbial community composition can strongly constrain permafrost biogeochemical processes. Here we tested how a model species of microarthropod (the Collembola Folsomia candida) affected aerobic CO2 production of permafrost soil over a 25 d incubation. By using Collembola stock cultures grown on permafrost soil or on an arctic topsoil, we aimed to assess the potential for endo- and ectozoochory of soil bacteria, while cultures grown on gypsum and sprayed with soil suspensions would allow the observation of only ectozoochory. The presence of Collembola introduced bacterial amplicon sequence variants (ASVs) absent in the no-Collembola control, regardless of their microbiome manipulation, when considering presence–absence metrics (unweighted UniFrac metrics), which resulted in increased species richness. However, these introduced ASVs did not induce changes in bacterial community composition as a whole (accounting for relative abundances, weighted UniFrac), which might only become detectable in the longer term. CO2 production was increased by 25.85 % in the presence of Collembola, about half of which could be attributed to Collembola respiration based on respiration rates measured in the absence of soil. We argue that the rest of the CO2 being respired can be considered a priming effect of the presence of Collembola, i.e. a stimulation of permafrost CO2 production in the presence of active microarthropod decomposers. Overall, our findings underline the importance of biotic interactions in permafrost biogeochemical processes and the need to explore the additive or interactive effects of other soil food web groups of which permafrost soils are deprived.

Dynamics of the intestinal bacterial community in black soldier fly larval guts and its influence on insect growth and development.

Black soldier fly (BSF), Hermetia illucens (Diptera: Stratiomyidae), is a prominent insect for the bioconversion of various organic wastes. As a saprotrophic insect, the BSF inhabits microbe-rich environments. However, the influences of the intestinal microorganisms on BSF growth and development are not very clear. In this study, the dynamics of the intestinal bacterial community of BSF larvae (BSFL) were analyzed using pyrosequencing. Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria were the most prevalent bacterial phyla in the intestines of all larval instars. The dynamic changes in bacterial community compositions among different larval instars were striking at the genus level. Klebsiella, Clostridium, Providencia, and Dysgonomonas were the relatively most abundant bacteria in the 1st- to 4th-instar BSFL, respectively. Dysgonomonas and Providencia also dominated the 5th- and 6th-instar larvae, at ratios of 31.1% and 47.2%, respectively. In total, 148 bacterial strains affiliated with 20 genera were isolated on different media under aerobic and anaerobic conditions. Among them, 6 bacteria, BSF1-BSF6, were selected for further study. The inoculation of the 6 isolates independently into germ-free BSFL feeding on an artificial diet showed that all the bacteria, except BSF4, significantly promoted BSF growth and development compared with the germ-free control. Citrobacter, Dysgonomonas, Klebsiella, Ochrobactrum, and Providencia promoted BSF development significantly by increasing the weight gains of larvae and pupae, as well as increasing the prepupae and eclosion rates. In addition, Citrobacter, Klebsiella and Providencia shortened the BSF life cycle significantly. The results illustrate the promotive effects of intestinal bacteria on BSF growth and development.

Soil Microbial and Organic Carbon Legacies of Pre-Existing Plants Drive Pioneer Tree Growth during Subalpine Forest Succession

Fast-growing pioneer tree species play a crucial role in triggering late successional development in forests. Experimental evidence of the soil legacy effects of pre-existing plants on pioneer tree performance is lacking. We explored the legacy effects of soils conditioned by early successional herbs (Poa poophagorum Bor and Potentilla fragarioides L.) and mid-successional shrubs (Rhododendron fortunei Lindl. and Enkianthus quinqueflorus Lour.) on late-successional ectomycorrhizal (ECM) pioneer tree (Betula platyphylla Sukaczev) seedling growth. The soils were analyzed for soil nutrient status and fungal and bacterial compositions using ITS and 16S rRNA gene sequencing. B. platyphylla seedlings produced higher biomass in soils conditioned by shrubs. Soil organic carbon (SOC) and bacterial and fungal legacies most impacted pioneer tree seedling growth. Additionally, the partial least squares path model revealed that soil nutrients, especially SOC, indirectly affected seedling biomass by their direct effects on the bacterial and fungal communities. The changes in bacterial community composition had a stronger effect on seedling biomass than those of fungi because bacteria with shorter turnover times are generally considered to be more efficient than fungi in enhancing nutrient availability. Our study integrates soil microbial and nutrient legacies to explain the potential mechanisms of pioneer tree regeneration.

Thermophilic Composting of Human Feces: Development of Bacterial Community Composition and Antimicrobial Resistance Gene Pool.

In times of climate change, practicing sustainable, climate-resilient, and productive agriculture is of primordial importance. Compost from different resources, now treated as wastes, could be one form of sustainable fertilizer creating a resilience of agriculture to the adverse effects of climate change. However, the safety of the produced compost regarding human pathogens, pharmaceuticals, and related resistance genes must be considered. We have assessed the effect of thermophilic composting of dry toilet contents, green cuttings, and straw, with and without biochar, on fecal indicators, the bacterial community, and antibiotic resistance genes (ARGs). Mature compost samples were analyzed regarding fecal indicator organisms, revealing low levels of Escherichia coli that are in line with German regulations for fertilizers. However, one finding of Salmonella spp. exceeded the threshold value. Cultivation of bacteria from the mature compost resulted in 200 isolates with 36.5% of biosafety level 2 (BSL-2) species. The majority is known as opportunistic pathogens that likewise occur in different environments. A quarter of the isolated BSL-2 strains exhibited multiresistance to different classes of antibiotics. Molecular analysis of total DNA before and after composting revealed changes in bacterial community composition and ARGs. 16S rRNA gene amplicon sequencing showed a decline of the two most abundant phyla Proteobacteria (start: 36–48%, end: 27–30%) and Firmicutes (start: 13–33%, end: 12–16%), whereas the abundance of Chloroflexi, Gemmatimonadetes, and Planctomycetes rose. Groups containing many human pathogens decreased during composting, like Pseudomonadales, Bacilli with Bacillus spp., or Staphylococcaceae and Enterococcaceae. Gene-specific PCR showed a decline in the number of detectable ARGs from 15 before to 8 after composting. The results reveal the importance of sufficiently high temperatures lasting for a sufficiently long period during the thermophilic phase of composting for reducing Salmonella to levels matching the criteria for fertilizers. However, most severe human pathogens that were targeted by isolation conditions were not detected. Cultivation-independent analyses also indicated a decline in bacterial orders comprising many pathogenic bacteria, as well as a decrease in ARGs. In summary, thermophilic composting could be a promising approach for producing hygienically safe organic fertilizer from ecological sanitation.

Aeration increases soil bacterial diversity and nutrient transformation under mulching-induced hypoxic conditions

Soil oxygen (O2) deficiency induced by organic mulching is easy to overlook. Aeration has been shown to potentially alleviate soil hypoxia stress. However, the responses of soil bacterial communities to such mulching-induced hypoxic conditions and aeration remain elusive. Therefore, a three-year field experiment, consisting of mulching (T1), mulching with aeration (TA1, poor aeration; TA2, strong aeration), and no-mulching (CK) treatments, was conducted in bamboo (Phyllostachys praecox) plantations. According to our results, the strong aeration treatment (TA2) alleviated soil acidification, increased soil nutrient availability, and significantly increased soil O2 content by 18.44% (P < 0.05) when compared with T1. In addition, TA2 significantly increased soil β-glucosidase, invertase, urease, and acid phosphatase activities compared with CK and T1 (P < 0.05). The alpha diversity indices with TA2 treatment were the highest, indicating that aeration increased the species richness and diversity of bacteria. The changes in bacterial community composition associated with TA2 treatment (i.e., an increase in Firmicutes, Verrucomicrobia, and Faecalibacterium abundance and a decrease in Chloroflexi and Bradyrhizobium abundance) were mainly related to nutrient and O2 content. Mantel Test results suggested that soil O2 content and temperature were the key factors shaping bacterial community composition. Structural equation modeling revealed that soil O2 content had a positive and direct influence on bacterial community diversity. Functional annotation of prokaryotic taxa predicted that TA2 significantly increased the relative abundance of bacterial communities associated with nitrification, nitrogen fixation, and ureolysis. Our results demonstrated that optimal soil aeration conditions (17.60% of O2 content) could enhance the diversity and function of soil bacterial communities. Overall, the findings of this study could serve as a benchmark for alleviating soil hypoxia caused by organic mulches, which is important for increasing the functionality of nutrient cycling bacterial communities in the soil.

Unraveling characterizations of bacterial community and spoilage profiles shift in chilled pork during refrigerated storage

Changes in bacterial community composition and bacterial counts of chilled pork during storage at 4 °C were unraveled by culture-dependent method and culture-independent method. Physical and chemical analyses including drip loss, total volatile basic nitrogen (TVB-N), pH, and surface color were also performed to estimate its quality and shelf life. A total of 37 phyla, 575 genera and 843 species were identified in all samples by high-throughput sequencing technology during 10 days’ storage. At the phylum level, Proteobacteria and Firmicutes were the dominant phylum. At the genus level, Pseudomonas spp., Acinetobacter spp., Pantoea spp., Brochothrix spp. and Raoultella spp. were the dominant genera with their average relative abundance above 5%. In addition, 12 species with average relative abundance more than 1% were found. These dominant bacteria were main pathogenic or spoilage bacteria, and seriously affected the quality of chilled meat. Based on the results of total viable counts (TVC), TVB-N level and sensory evaluation, the shelf life of chilled pork stored at 4 °C was no more than 3 days. Through the analyses of the TVC and the microbial community structure during the spoilage of chilled pork, the main microorganisms causing spoilage were revealed, which will guide significance for further control microbial quality of chilled pork.

Identification of key bacterial players during successful full-scale soil field bioremediation in Antarctica

The Antarctic continent is not exempted from anthropogenic contamination. Diesel spills on Antarctic soils occur frequently. There, extreme climate conditions and the scarce infrastructure, cause that few remediation strategies become feasible. Bioremediation has proven to be an effective approach for hydrocarbon-contaminated soils in Antarctica, allowing the removal of up to 80% of the contaminant by biostimulating soil microbial communities in biopiles. However, little is known on the changes that this treatment cause in the microbial communities, and how may this knowledge be used for future bioremediation schemes. In this work, we analyzed the changes in the bacterial community composition of biostimulated (BS) and control (CC) biopiles at Carlini Station (Arg.), Antarctica, from our previously reported “on-site” bioremediation scheme. The results showed that hydrocarbon biodegradation in Antarctic soils was accompanied by a significant change in bacterial community composition, with a progressive differentiation between the treated (BS) and non-treated (CC) systems as a function of time. Microbial diversity decreased in the BS system due to the enrichment in genera Pseudomonas, Rhodococcus, and Rhodanobacter, that seemed to follow an r/K (or copiotrophic/oligotrophic) strategist dynamic, in which Pseudomonas increased significantly at the early stages of the treatment (from initial 23.8% up to 33.2% at day 20, r strategist), while Rhodococcus and Rhodanobacter (K strategists) became dominant since day 20 and until the end of the experiment (from 5.4% to 2.4% at T = 0 days, up to 17.4% and 14.0% at the end of the experiment, respectively). In the control system, Sphingomonas (14.0% at T = 30 days), Pseudomonas (10.5% at T = 30 days), and Rhizorhapis (9.9% at T = 30 days) were the genera with higher relative abundance during the entire treatment period, with no short-term shifts in dominances and a more diverse and even bacterial community.

Soil pH and aridity influence distributions of branched tetraether lipids in grassland soils along an aridity transect

Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are membrane lipids of certain soil bacteria, and their relative distributions are used as a proxy for air temperature and soil pH. While temperature is recorded by the degree of methylation, soil pH is reflected by the amount of internal cyclization and the relative abundance of 6-methyl isomers. Since the exact producers of brGDGTs remain enigmatic, the mechanisms underlying their empirical relationships with temperature and soil pH, and thus the reliability of brGDGT-based paleorecords, are not well understood, especially in arid regions where mean annual precipitation (MAP) is less than 500 mm. Here, we evaluate the influence of soil pH and aridity on brGDGT distributions in grassland soils along an aridity transect (MAP = 173–415 mm) in Inner Mongolia. While the absolute and fractional abundance of 6-methyl brGDGTs increases with increasing soil pH and aridity, following the trend in the global surface soil calibration dataset, the degree of cyclization does not. This indicates that in arid regions, soil pH reconstructions based on the relative contribution of 6-methyl brGDGTs are likely more reliable than those based on the degree of cyclization. Furthermore, 5- and 6-methyl brGDGTs respond differently to aridity, supporting prior suggestions that the distribution of brGDGTs could be the result of changes in bacterial community composition instead of the direct physiological alteration of molecular structures by the source organisms. Analysis of the bacterial community composition in the same soil transect indicates that the relative abundance of Acidobacteria, the phylum hosting potential brGDGT source-organisms, shows a poor relationship with aridity. Instead, Verrucomicrobia (r2 = 0.70, p < 0.01), and its subclass Spartobacteria (r2 = 0.70, p < 0.01) in particular, show a significant negative correlation with aridity, resembling that of 5-methyl brGDGTs. Similarly, Actinobacteria are positively correlated with aridity (r2 = 0.59, p < 0.01), following the same trend as that of 6-methyl brGDGTs. The ability of certain cultures of Verrucomicrobia and Actinobacteria to produce iso-C15:0 fatty acids that could serve as building blocks for brGDGTs hints that Verrucomicrobia and Actinobacteria could possibly produce brGDGTs in arid soils.