Similar Bacterial Communities Research Articles

Fe(III) oxide microparticles modulate extracellular electron transfer in anodic biofilms dominated by bacteria of the Pelobacter genus

Exo-electrogenic microorganisms have been extensively studied for their ability to transfer electrons with solid surfaces using a large variety of metabolic pathways. Most of the studies on these microorganisms consist in the replacement of solid electron acceptors such as Fe(III) oxides found in nature by electrodes with the objective of generating harvestable current in devices such as microbial fuel cells. In this study we show how the presence of solid ferric oxide (Fe2O3) particles in the inoculum during bio-anode development influences extracellular electron transfer to the electrode. Amplification and sequencing of the 16S rRNA (V4-V5 region) show bacteria and archaea communities with a large predominance of the Pelobacter genus, which is known to be phylogenetically close to the Geobacter genus, regardless of the presence or absence of ferric oxide in the inoculum. Data indicate that the bacteria at the bio-anode surface can preferentially utilize solid ferric oxide as terminal electron acceptors instead of the anode, though extracellular electron transfer to the anode can be restored by removing the particles. Mixed inoculum commonly used to develop bioanodes may produce similar bacterial communities with divergent electrochemical responses due to the presence of alternate electron acceptors, with direct implications for microbial fuel cell performance.

A closer look into the microbiome of microalgal cultures.

Although bacteria are commonly co-occurring in microalgal cultivation and production systems, little is known about their community structure and how it might be affected by specific microalgal groups or growth conditions. A better understanding about the underlying factors that determine the growth of specific bacterial populations is not only important for optimizing microalgal production processes, but also in the context of product quality when the algal biomass is to be used for future food or feed. We analyzed the bacterial community composition associated with nine microalgal strains in stock culture, maintained in two different growth media, to explore how specific taxonomic microalgal groups, microalgal origin, or the growth medium affect the bacterial community composition. Furthermore, we monitored the bacterial community composition for three Phaeodactylum strains during batch cultivation in bubble columns to examine if the bacterial composition alters during cultivation. Our results reveal that different microalgal genera, kept at the same cultivation conditions over many years, displayed separate and unique bacterial communities, and that different strains of the same genus had very similar bacterial community compositions, despite originating from different habitats. However, when maintained in a different growth medium, the bacterial composition changed for some. During batch cultivation, the bacterial community structure remained relatively stable for each Phaeodactylum strain. This indicates that microalgae seem to impact the development of the associated bacterial communities and that different microalgal genera could create distinct conditions that select for dominance of specific bacteria. However, other factors such as the composition of growth medium also affect the formation of the bacterial community structure.

Response of Intestinal Microbiota of Tiger Puffer (Takifugu rubripes) to the Fish Oil Finishing Strategy

The fish oil finishing (FOF) strategy, that is, re-feeding fish with fish oil (FO)-based diet after a certain period of feeding with alternative lipid source-based diets. On tiger puffer, the present study investigated the response of intestinal microbiota to FOF. Fish were fed four diets based on FO, soybean oil, palm oil and beef tallow as lipid sources, respectively, firstly for 50 days (growing-out period), and then fed the FO-based diet for 30 more days (FOF period). The results showed that dietary terrestrially sourced oils impaired the intestinal function in the growing-out period. However, the activities of amylase, trypsin and anti-oxidative enzymes (SOD, CAT, T-AOC), as well as gene expression of inflammatory cytokines (IL-1β, TNF-α, TGF-β) and tight junction protein (Claudin4, Claudin7, Claudin18, JAM, ZO-1) in the intestine were significantly recovered by FOF. The 16S rDNA sequencing analysis showed that FOF improved the similarity of bacterial community among the groups. The MetaStat analysis confirmed that FOF regulated the abundance of butyric acid-producing bacteria (Lachnospiraceae, Eubacterium, Butyricicoccus, Clostridium and Roseburia) and bacteria related to digestion and absorption (Sphingomonas, Romboutsia and Brevibacillus). In conclusion, FOF can recover the intestine function. The intestinal microbiota probably participated in and played a key role in the recovery process.

Microbiome analysis of raw honey reveals important factors influencing the bacterial and fungal communities.

Raw honeys contain diverse microbial communities. Previous studies have focused on isolating bacteria and fungi that are culturable, while missing a large proportion of the microbial community due to culture-based constraints. This study utilized next-generation sequencing (NGS) to analyze the composition of microorganisms in raw honey; these data can reveal environmental and physicochemical variables that are associated with different microbial communities. To examine the microbial composition (bacteria and fungi) of raw honey and analyze its association with physicochemical properties, four types of honey (monofloral, wildflower, manuka, and feral; n total = 36) were analyzed via amplicon metagenomics. The analyzed honey samples had relatively similar bacterial communities but more distinct and diverse fungal communities. Honey type was determined as a significant factor influencing alpha and beta diversity metrics of bacterial and fungal communities. For the bacterial communities, titratable acidity (TA) was associated with community richness and diversity. For the fungal communities, Brix, TA, and color were associated with community richness, while water activity and color were associated with community diversity. Additionally, important bacterial and fungal amplicon sequence variants (ASVs) that influenced the overall community were identified. Results from this study provide important insights into the microbial communities associated with different types of raw honey, which could improve our understanding of microbial dynamics in beehives, improve honey production, and prevent honeybee disease.

Investigation of systemic granulomatosis in cultured meagre, Argyrosomus regius, using clinical metagenomics

Systemic granulomatosis is a peculiar disease of unknown etiology affecting meagre, Argyrosomus regius, an important aquaculture fish species. Several pathogenic microorganisms have been suggested as causative agents. In this study, we have applied amplicon metagenomics of the 16S rRNA gene in kidneys of fish exhibiting different health states, ranging from apparently healthy to kidneys with calcification. Comparison of the kidney microbiomes of the different fish groups showed that all fish had similar bacterial communities. Linear discriminant analysis effect size revealed only three OTUs significantly enriched in the sick individuals, with no known granuloma-causing species being present among them, reinforcing the hypothesis of a non-infectious cause of the disease in this fish species.

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

Geographical variation of bacterial and ciliophoran communities in tidal flats in a continental archipelago.

In tidal flats, which are located at the transition zone between terrestrial and marine ecosystems, environmental factors such as temperature, sediment particle size, and tidal range exhibit geographic variation. Accordingly, the composition and structure of the microbial communities in the tidal flats are likely to vary in geographically different habitats. To clarify these differences with environmental factors causing them, we analyzed microbial communities consisting of bacteria and ciliates in sediments collected from nine tidal flats in geographical diverse region from Hokkaido to Kagoshima, Japan. The results confirmed that the community structures of bacteria and ciliophora in tidal flat sediments differed at the geographical scale of the Japanese archipelago. However, the variation could not be explained by the physical distance between the tidal flats nor by the differences in the trophic conditions among the tidal flats. Instead, the OTU richness of both the bacterial and ciliophoran communities was significantly related to the tidal range. The results also showed that bacteria and ciliophora tended to form similar communities among the tidal flats with similar median particle sizes. Furthermore, ciliophoran communities were similar among the tidal flats with similar bacterial communities. The results suggest that bacteria and ciliophora interact each other through trophic relationships or physical and chemical processes in the sediment habitats.

Compositional responses of aquatic bacterial communities and their network interactions to phytoplankton-derived dissolved organic matter from freshwater ponds

Bacteria play a central role in the degradation of phytoplankton-derived dissolved organic matter (P-DOM) particularly in algal-blooming aquatic systems; yet our understanding of the interaction between bacteria and P-DOM is still poor. We supplied differential P-DOM that varied in concentration and molecular weight (released from distinct phytoplankton collected from blue-green algal-blooming grass carp Ctenopharyngodon idellus farming ponds) to similar aquatic bacterial communities (isolated from non-blooming grass carp ponds), to explore how P-DOM affects bacterial community dynamics and to identify the most responsive degrading taxa using UV-visible absorption spectroscopy and high-throughput sequencing. Bacterial cultures all had similar degradation effects upon P-DOM, causing decreases in its concentration but increases in its molecular weight and aromaticity. In contrast, bacterial compositional changes varied primarily depending on P-DOM molecular weight, and Bacteroidia taxa were mostly affected, appearing more adapted to metabolize high-molecular-weight P-DOM. Nevertheless, most of the degrading taxa were recurrent and typically members within Gammaproteobacteria and Bacilli, indicating substrate-controlled bacterial responses induced by P-DOM. Network analysis revealed that bacterial communities harbored relatively low-abundant degrading members rather than dominant ones as keystone taxa, which presented simultaneously crucial microbial connections within communities and strong associations with environments and therefore played an over proportional role in maintaining community stability and functioning. Moreover, the keystone taxa may be generalists, and their ecological attributes can be described by oligotrophs that correspond to the K-strategists. Generally, this study implied a pivotal role of Gammaproteobacteria, particularly Pseudomonas, in P-DOM biodegradation, most probably in algal-blooming aquatic environments.

Bacterial Diversity and Community Structure Characteristics in Rhizosphere Soil of Coconut (Cocos nucifera L.) under Intercropping Pineapple

To explore the bacterial diversity and community structure characteristics of the rhizosphere soil of fruit type coconuts of different varieties under the intercropping pineapple model, the Illumina high throughput sequencing technology was used to detect the composition and diversity of soil microorganisms. Furthermore, the correlation between the physical and chemical properties of soil and the characteristics of the rhizosphere soil community was analyzed. The contents of OM, EC, AN, AP, AK, ACa, and AMg in coconut rhizosphere soil under intercropping were significantly higher than those under coconut monocropping. However, the soil pH value of the intercropping mode decreased significantly. The diversity of bacteria in the rhizosphere soil of coconut intercropped pineapple was higher than that of coconut monocropped. The diversity of bacteria in the rhizosphere soil of different varieties of coconuts was also different: The order of bacterial diversity was JG > JYT > JYO > JH. The dominant bacteria of the rhizosphere soil, in order, were Proteobacteria, Acidobacteriota, Bacteroidota, Verrucomicrobiota, Actinobacteria, Planctomycota, Firmicutes, Gemmatimonadota, Myxococcota, Nitrospirota, which indicated that the composition of bacterial species between intercropping and monocropping was very different. JG, JYO, and JYT had a high similarity of bacterial community through principal component analysis and cluster analysis, and the bacterial community composition of these three treatments was significantly different from that of CH and JH. In addition, JH had significant differences in bacterial community composition compared to CH. This also showed that different varieties of coconut intercropping pineapple have a great impact on the bacterial composition of coconut rhizosphere soil.

Composition and assembly of the bacterial community in the overlying waters of the coral reef of China's Xisha Islands.

Coral reef ecosystems are one of the most diverse and productive habitats on Earth. Microbes in the reef-overlying waters are key players in maintaining this ecosystem through regulating biogeochemical and ecological processes. However, the composition structure and assembly mechanism of microbial community in the reef-overlying waters remain largely unknown. In the present study, the bacterial communities from the overlying waters of atolls and fringing reefs as well as the surface waters of the adjacent open ocean of the Xisha Islands in the South China Sea were investigated using 16S rRNA high-throughput sequencing combined with a size-fractionation strategy. The results showed that environments of all sampling stations were similar, characterized by an almost complete lack of inorganic nutrients such as nitrogen and phosphorus. Proteobacteria, Cyanobacteria and Bacteroidetes were the dominant phyla, and Synechococcus was most abundant at the genus level in both large fraction (LF; 1.6-200 μm) and small fraction (SF; 0.2-1.6 μm) communities. Only a slight difference in community composition between LF and SF samples was observed. The bacterial communities among the three habitat types showed noticeable differences, and the bacterial composition among the atoll reefs was more varied than that among the fringing reefs. The similarity of bacterial communities significantly declined with the increasing geographic distance, and stochastic processes were more important than deterministic processes in bacterial community assembly. This study sheds lights on the bacterial biodiversity of coral reefs and the importance of stochastic process in structuring bacterial communities.

Dispersal limitation and host selection drive geo-specific and plant-specific differentiation of soil bacterial communities in the Tibetan alpine ecosystem

Soil bacteria, which are active in shrub encroachment, play key roles in regulating ecosystem structure and function. However, the differentiation characteristics and assembly process of bacterial communities in scrubbed grasslands remain unknown. Taking the Qinghai-Tibet Plateau, a hotspot of shrub encroachment, as the study area, we collected 192 soils near nine natural typical shrubs' roots on a trans-longitude transect (about 1800 km) and investigated the bacterial communities using 16S rRNA amplicon sequencing. We found that the bacterial communities exhibited plant-specific and geographic-specific differentiation. On the one hand, bacterial communities differed significantly across plant species, with widely distributed shrubs harboring high diversity communities but few plant-specific taxa, and narrowly distributed shrubs possessing low diversity communities but more plant-specific taxa. Besides, there was a significant negative correlation between bacterial community similarity and plant phylogenetic distance. On the other hand, bacterial communities differed across geographic sites, with a significant decay in bacterial community similarity with geographic distance. The bacterial alpha diversity varied in an inverted V-shape from west to east, peaking at 91°E, which could be largely driven by mean annual temperature, soil pH and soil total carbon content. Community differentiation increased with the heterogeneity degree of assembly processes, and the dominant assembly process in these two specific differentiations differed. Dominated by stochastic and deterministic forces, respectively, geography diverged bacterial communities primarily through increased dispersal limitation, whereas plants diverged bacterial communities primarily through increased variable selection. Our study provides new insight into the characteristics and mechanisms of root-surrounding soil bacteria differentiation in scrubbed grasslands, contributing to the scientific management of degraded grasslands and the prediction of bacterial community structure and ecosystem function in response to global change.

Aphid species specializing on milkweed harbor taxonomically similar bacterial communities that differ in richness and relative abundance of core symbionts

Host plant range is arguably one of the most important factors shaping microbial communities associated with insect herbivores. However, it is unclear whether host plant specialization limits microbial community diversity or to what extent herbivores sharing a common host plant evolve similar microbiomes. To investigate whether variation in host plant range influences the assembly of core herbivore symbiont populations we compared bacterial diversity across three milkweed aphid species (Aphisnerii, Aphis asclepiadis, Myzocallis asclepiadis) feeding on a common host plant (Asclepias syriaca) using 16S rRNA metabarcoding. Overall, although there was significant overlap in taxa detected across all three aphid species (i.e. similar composition), some structural differences were identified within communities. Each aphid species harbored bacterial communities that varied in terms of richness and relative abundance of key symbionts. However, bacterial community diversity did not vary with degree of aphid host plant specialization. Interestingly, the narrow specialist A.asclepiadis harbored significantly higher relative abundances of the facultative symbiont Arsenophonus compared to the other two aphid species. Although many low abundance microbes were shared across all milkweed aphids, key differences in symbiotic partnerships were observed that could influence host physiology or additional ecological variation in traits that are microbially-mediated. Overall, this study suggests overlap in host plant range can select for taxonomically similar microbiomes across herbivore species, but variation in core aphid symbionts within these communities may still occur.

Biogeographical patterns and drivers of bacterial community in the Qinghai-Tibetan Plateau

Qinghai-Tibetan Plateau (QTP) has been ranked as one of the main hotspots of biodiversity. The biogeographic research on soil bacteria lags behind that of animals and plants, especially on the QTP. In this paper, we explored soil bacterial communities across two alpine grassland ecosystems (alpine steppe and alpine meadow) on QTP in China. Bacterial α-diversity differ significantly, which could be attributed to changes in plant cover and total phosphorus (TP) content. The dominant bacterial phyla were Actinobacteriota (28.54 %), Proteobacteria (22.74 %) and Acidobacteriota (12.96 %). Obvious distance-decay of bacterial community was observed across environmental factors and geographic distance (P < 0.001). Partial Mantel tests indicated that differences of bacterial community in whole data and alpine steppe were driven by the joint impacts of environmental factors and geographic distance, while differences of bacterial community in alpine meadow were driven by a sole impact of geographic distance. The MRM model explained 57.2 % and 49.4 % of the variability in the whole data and alpine meadow, respectively (P < 0.001), with pH being the most important variables explaining the similarity of bacterial community, followed by geographic distance, available phosphorus (AP) content and C/N. In addition, 25.6 % of the variability in alpine steppe was explained by the MRM model (P < 0.001), with geographic distance being the most important variables explaining the similarity of bacterial community. In summary, our findings suggested that α-diversity patterns, and the driving factors of the bacterial community structure were different across two ecosystem types, and environmental factors and geographic distance played different roles on the bacterial community structure in alpine steppe and alpine meadow. This study provides new understanding of soil microbial geography, and ecosystem functions driven by soil bacteria.

The Effect of Date Palm Genotypes on Rhizobacterial Community Structures under Saline Environments.

Some genotypes of date palms (Phoenix dactylifera L.) are salt-tolerant; however, salinity significantly affects others. This study aimed to determine the root epiphytic bacterial contributions to the salt tolerance mechanism in the date palm and to verify if the salt-tolerant "Umsila" and the salt-susceptible "Zabad" cultivars have different bacterial communities. Therefore, the epiphytic bacterial community structures were investigated in both cultivars when grown under control and salinity conditions. The proximal soils of the roots were collected, the DNA was extracted, and a culture-independent approach using Illumina® MiSeq™ sequence analysis was carried out to identify the changes in the bacterial community structures in the soil samples due to the changes in salinity and the genotypes of the plants based on 16S rRNA gene sequencing. While salt tolerance response differences were evident between the two cultivars, the 16S rRNA gene sequencing results revealed 771 operational taxonomic units (OTUs), including 62 that were differentially accumulated in response to salinity. The ordination analysis showed significant (p = 0.001) changes among the communities in response to salinity in both cultivars. However, the results showed that the two cultivars had distinct bacterial communities when grown under controlled conditions, whereas they had a more similar bacterial community structure when grown under salinity conditions. The plant genotype does not affect the epiphyte bacterial community structure under salinity, probably because salinity affects the plant-microbe interaction similarly in both cultivars. Also, the identified rhizospheric bacteria are not directly associated with the root's physiological processes in response to salinity.

Evaluation of the Ecological Environment Affected by Cry1Ah1 in Poplar.

Populus is a genus of globally significant plantation trees used widely in industrial and agricultural production. Poplars are easily damaged by Micromelalopha troglodyta and Hyphantria cunea, resulting in decreasing quality. Bt toxin-encoded by the Cry gene has been widely adopted in poplar breeding because of its strong insect resistance. There is still no comprehensive and sufficient information about the effects of Cry1Ah1-modified (CM) poplars on the ecological environment. Here, we sampled the rhizosphere soils of field-grown CM and non-transgenic (NT) poplars and applied 16S rRNA and internal transcribed spacer amplicon Illumina MiSeq sequencing to determine the bacterial community associated with the CM and NT poplars. Based on the high-throughput sequencing of samples, we found that the predominant taxa included Proteobacteria (about 40% of the total bacteria), Acidobacteria (about 20% of the total bacteria), and Actinobacteria (about 20% of the total bacteria) collected from the natural rhizosphere of NT and CM poplars. In addition, studies on the microbial diversity of poplar showed that Cry1Ah1 expression has no significant influence on rhizosphere soil alkaline nitrogen, but significantly affects soil phosphorus, soil microbial biomass nitrogen, and carbon. The results exhibited a similar bacterial community structure between CM varieties affected by the expression of Cry1Ah1 and non-transgenic poplars. In addition, Cry1Ah1 expression revealed no significant influence on the composition of rhizosphere microbiomes. These results broadly reflect the effect of the Bt toxin-encoded by Cry1Ah1 on the ecology and environment and provide a clear path for researchers to continue research in this field in the future.

Increased similarity of aquatic bacterial communities of different origin after antibiotic disturbance

Stochastic or deterministic processes control the bacterial community assembly in waters and their understanding is a fundamental question to correctly manage aquatic environments exposed to the release of antibiotics from anthropogenic sources. It has been suggested that microdiversity (i.e. the rare biosphere) convers freshwater communities with stability, meaning that previously rare taxa bloom when the community is disturbed. Since there might be a seed bank of similar, but not abundant, bacterial taxa in different waters, we tested whether a disturbance by an antibiotic cocktail would increase similarity in bacterial communities from different freshwater systems (a wastewater effluent and two lakes). In a continuous culture set-up in chemostats, we show that disturbance with antibiotics causes communities from different environments to become more similar. Once the antibiotic pressure is released the communities tend to become more dissimilar again. This shows that there is a similar shift in community composition even in waters from very different origins when they are disturbed by antibiotics, even at low concentrations. Antibiotics impact the bacterial communities at the cell and the community level, independently by the original degree of anthropogenic stress they are adapted to, altering the original phenotypes, genotypes, and the relations between bacteria.

Effects of different colored polyethylene mulching films on bacterial communities from soil during enrichment incubation

Studies have shown that mulching agricultural fields with plastic residues can influence microbial communities in the environment, but few studies have investigated the differences in the soil microbial communities in distinct areas under mulching with different colored plastic products. Thus, in this study, we explored how different colored polyethylene mulching films (PMFs) might affect soil bacterial communities during enrichment incubation. We found significant differences in the bacterial communities under different colored PMFs after incubation. Treatment with the same colored PMF obtained more similar bacterial community compositions. For instance, at the class level, Gammaproteobacteria and Bacteroidia were most abundant with black PMF, whereas Actinobacteria and Bacteroidia were most abundant with white PMF. The most abundant genera were Acinetobacter and Chryseobacterium with black PMF but Rhodanobacter and Paenarthrobacter with white PMF. Polyethylene- and hydrocarbon-degrading bacteria were the core members detected under both treatments, and the bacterial communities were predicted to have the potential for the biodegradation and metabolism of xenobiotics after enrichment culture according to the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) tool. In addition, the bacterial communities in soil from Xinjiang treated with white PMF and in soil from Yangling treated with black PMF were strongly correlated and stable. Our results suggest that the color of the PMF applied affected the soil bacterial communities, where plastics with the same color may have recruited similar species of microorganisms, although the origins of these microorganisms were not the same.

Deciphering environmental factors driving soil microbial elevational distribution in the southeastern Qinghai-Tibetan Plateau

Qinghai-Tibetan Plateau (QTP) has been ranked as one of the main hotspots of biodiversity. Many studies on microbial diversity and structure have been investigated in QTP, whereas the joint impacts of environmental properties and geographic distance that influence microbial communities along altitudinal gradient is yet poorly understood. In this paper, we investigated sites along the elevational gradient of 3270–4530 m on the southeast QTP in China, characterizing environmental properties, and systematically examined the composition, diversity patterns and the driving factors of soil microbial community structures. Elevation led to distinct changes in environmental properties. Bacterial α-diversity did not differ significantly among elevations, whereas fungal α-diversity showed a decrease pattern, which could be attributed to changes in temperature, soil moisture, pH and total carbon content. The dominant bacterial and fungal phyla were Actinobacteria (30.4%), Proteobacteria (24.1%) and Acidobacteria (14.7%), and Ascomycota (52.3%), Basidiomycota (32.6%) and Mortierellomycota (13.9%), respectively. Notable distance-decay of microbial community was observed across environmental factors and geographic distance. Partial Mantel tests indicated that differences in bacterial community were driven by the joint impacts of environmental factors and geographic distance, while differences in fungal community were primarily driven by a sole impact of environmental factors. The multiple regression on matrices (MRM) model explained 79% of the variability in bacterial community similarity, with pH being the most important variables, followed by soil moisture, elevation, AK content and geographic distance. The proportion of variance explained by MRM model was 55%, with elevation and TN content being the main variables altering the soil fungal structure. In summary, our findings suggested that α-diversity patterns, and the driving factors of the bacterial and fungal community structure were different, and environmental factors and geographic distance played different roles on the bacterial and fungal community structures.

Mature biofloc harbor similar bacterial communities regardless of the vegetal floating substrates (oat, amaranth, or wheat) used as promoters

Mature biofloc harbor similar bacterial communities regardless of the vegetal floating substrates (oat, amaranth, or wheat) used as promoters

Factors associated with soils suppressive to black scurf of potato caused by Rhizoctonia solani

Soils in which disease fails to develop despite pathogen presence are considered disease-suppressive. They offer sustainable, effective protection to plants against infection by soil-borne pathogens. Naturally disease-suppressive soils have been reported for diseases of a diverse range of agricultural crops worldwide yet the underlying mechanisms of disease suppression are still not completely understood. Two large greenhouse experiments, conducted during 2017/18 (Year 1) and 2018/19 (Year 2), determined that soils naturally suppressive to stem canker and black scurf of potato (caused by Rhizoctonia solani) are present in vegetable-arable cropping soils of the Auckland and Waikato regions of New Zealand. Soil was pre-treated with heat prior to inoculation with R. solani and compared with untreated and uninoculated controls to ascertain if stem canker and black scurf suppression was ‘general’, or ‘specific’ (i.e. transferable; possibly involving specific microorganisms). Rhizoctonia solani inoculation was also combined with transfer of one part test soil to nine parts of a known disease-conducive soil. Abiotic factors such as soil texture and organic matter content influenced black scurf incidence and severity. Soil microorganisms were also involved in disease suppression since black scurf incidence and severity markedly increased when they were eliminated or reduced by soil heat pre-treatment. Microbial profiling of the soils through sequencing revealed that taxa of geographically close soils of the same type had similar fungal and bacterial community structure and diversity even though they differed in their capacity to suppress black scurf. These results suggest that although the soil microbiome as a whole, was mainly responsible for soil disease suppressiveness, certain bacterial genera or species may play a role in black scurf suppression.