Microbial Community Functional Diversity Research Articles

Community Level Physiological Profiling of Microbial Communities Influencing Mine Spoil Genesis in Chronosequence Coal Mine Overburden Spoil

Ecological restoration through mine spoil genesis should be dogmatic and the strategies involved a holistic approach, which emphasizes the role of microbial community composition that varies in accordance with the physiological and nutritional status of mine spoil profiles. This is because the patterns observed aboveground is being driven by the belowground diversity and processes. Thus, the relationship between microbial community structure and mine spoil genesis in chronosequence coal mine spoil has attracted considerable research attention. The occurrence of higher microbial diversity and difficulties in culturing microbes necessitate the use of a culture-independent approach through community-level physiological profiling based on the patterns of carbon source utilization using BIOLOG Ecoplate and thereby the functional diversity of microbial communities in different age series coal mine spoil was determined. The average well-color development exhibited an increasing trend with a minimum in OB0 (0.0640) and a maximum in OB15 (0.5060) over time. The patterns of substrate utilization (carbohydrates, carboxylic and ketonic acids, amino acids, polymers, amines, and amides) reflect the shift in microbial community composition in different age series coal mine spoil over time. Gradual increase in species richness and Shannon diversity index with the increase in age of mine spoil substantiated relatively higher microbial diversity reflecting the sign of mine spoil genesis. Principal component analysis and redundancy analysis based on the differential patterns of substrate utilization discriminate different age series coal mine spoil into independent clusters, which evaluated the broad-scale patterns of microbial community dynamics influencing the pace and progress of mine spoil genesis.

Effects of Straw Returning on Soil Chemical Properties and Microbial Community Diversity under the Rice-Crayfish Integrated System

This study presents an investigation of soil chemical properties and microbial community diversity by Biolog ECO analysis in a seven-year field experiment using winter flooded fallow + no straw returning (W), winter flooded fallow + straw returning (WS), and winter flooded fallow + straw returning + crayfish farming (WSC) at soil depths of 0–10 cm and 10–20 cm. Compared with the WS treatment, the WSC treatment had significantly higher total organic carbon (TOC) content in the 0–10 cm layer as well as greater available nitrogen (AN) and total nitrogen (TN) contents and acid phosphatase and sucrase activities in the 10–20 cm layer, while the pH value, total reducing substances, and Fe2+ content in the 0–20 cm layer were considerably lower. The WSC treatment improved the microbial species abundance in the 10–20 cm layer and the utilization rate of carbon sources in the 0–20 cm layer compared with the WS treatment. The soil microbial species abundance, microbial community diversity, and utilization rate of carbon sources in all of the layers examined were significantly higher in the WSC treatment than in the W treatment. The results indicate that straw returning under the rice-crayfish integrated system improves the contents of TOC, TN, and AN, decreases reducing substances properties, increases acid phosphatase and sucrase activities, and improves microbial community functional diversity, thereby contributing to the improvement of soil quality and the long-term sustainable development of the rice-crayfish integrated system.

Effects of Nitrogen Addition on Soil Microbial Functional Diversity and Extracellular Enzyme Activities in Greenhouse Cucumber Cultivation

Greenhouses, commonly used for vegetable production, are experiencing large nitrogen (N) inputs in North China, which leads to soil acidification, increases soil N availability, and affects microbial community structure and composition. However, it remains unclear how N enrichment influences soil microbial functional activities in this region. In this study, we conducted a two-year pot experiment in a greenhouse to evaluate the effects of four different rates of N addition (0, 334, 668, and 1002 kg N ha−1 year−1) on cucumber soil properties, extracellular enzyme activities, and community level physiological profiles (CLPP). We found that high-N addition (1002 kg N ha−1) caused a massive accumulation of inorganic nitrogen and soil acidification, which was not beneficial to soil microbial activities. The color development (AWCD) values for the metabolism of microbial carbon sources and the activities of soil extracellular enzymes also showed a significant decrease in high N(N3) treatment. Additionally, the activity of leucine aminopeptidase (LAP) and polyphenol oxidase (PPO) of N3 decreased by 36% and 50% compared to the N0 and could be a good predictor for microbial functional diversity and microbial biomass carbon (MBC). Structural equation modeling (SEM) confirmed that the reduction of microbial functional diversity is mainly coregulated by the decline of soil pH and the change of cucumber BGB (belowground biomass) resulting from soil C and N imbalance. Overall, excessive N-fertilizer amendment can be more dangerous to microbial community functional diversity, especially for carbohydrate utilization which adversely affects cucumber yield in current intensive management.

Effects of Insect-Resistant Maize 2A-7 Expressing mCry1Ab and mCry2Ab on the Soil Ecosystem.

Transgenic maize 2A-7 expressing mCry1Ab and mCry2Ab has excellent resistance to lepidopteran pests. Previous studies have investigated the effects of several Bacillus thuringiensis (Bt) proteins on the soil. However, the effects of artificially modified Bt proteins on soil ecosystems are still unclear. To evaluate the effects of transgenic maize 2A-7 on soil, the physicochemical properties, enzyme activities and functional diversities of the microbial communities in rhizosphere soils from 2A-7 and its near-isogenic non-transgenic control Dongdan 6531 were analyzed at different developmental stages under field conditions. The alteration of six physicochemical properties (pH, total nitrogen, total phosphorus, organic matter, available phosphorus and alkali-hydrolyzed nitrogen) and six functional enzymes (catalase, alkaline phosphatase, sucrase, acid phosphatase, urease and alkaline protease) activities in the rhizosphere soils between the two maize cultivars were drastically correlated with plant growth stage, but not affected by the artificially modified Bt transgenes. An analysis of time-course Biolog data revealed that the functional diversity of microbial communities in the rhizosphere soil of 2A-7 and its control were similar at each developmental stage. The results suggest that transgenic maize 2A-7 has no significant impact on the soil ecosystem and provide valuable information on scientific safety assessments of 2A-7 and its commercial applications.

Functional Diversity of Microbial Communities in the Soybean (Glycine max L.) Rhizosphere from Free State, South Africa.

The plant microbiome is involved in enhancing nutrient acquisition, plant growth, stress tolerance, and reducing chemical inputs. The identification of microbial functional diversity offers the chance to evaluate and engineer them for various agricultural processes. Using a shotgun metagenomics technique, this study examined the functional diversity and metabolic potentials of microbial communities in the rhizosphere of soybean genotype link 678. The dominant genera are Geobacter, Nitrobacter, Burkholderia, Candidatus, Bradyrhizobium and Streptomyces. Twenty-one functional categories were present, with fourteen of the functions being dominant in all samples. The dominant functions include carbohydrates, fatty acids, lipids and isoprenoids, amino acids and derivatives, sulfur metabolism, and nitrogen metabolism. A Kruskal–Wallis test was used to test samples’ diversity differences. There was a significant difference in the alpha diversity. ANOSIM was used to analyze the similarities of the samples and there were significant differences between the samples. Phosphorus had the highest contribution of 64.3% and was more prominent among the soil properties that influence the functional diversity of the samples. Given the functional groups reported in this study, soil characteristics impact the functional role of the rhizospheric microbiome of soybean.

Microbial Community, Metabolic Potential and Seasonality of Endosphere Microbiota Associated with Leaves of the Bioenergy Tree Paulownia elongata × fortunei.

The microbial structure and metabolic function of plant-associated endophytes play a key role in the ecology of various environments, including trees. Here, the structure and functional profiles of the endophytic bacterial community, associated with Paulownia elongata × fortunei, in correlation with seasonality, were evaluated using Biolog EcoPlates. Biolog EcoPlates was used to analyse the functional diversity of the microbiome. The total communities of leaf endophyte communities were investigated using 16S rRNA V5–V7 region amplicon deep sequencing via Illumina MiSeq. Community level physiological profiling (CLPP) analysis by the Biolog EcoPlate™ assay revealed that the carboxylic acids (19.67–36.18%) and amino acids (23.95–35.66%) were preferred by all by all communities, whereas amines and amides (0.38–9.46%) were least used. Seasonal differences in substrate use were also found. Based on the sequencing data, mainly phyla Proteobacteria (18.4–97.1%) and Actinobacteria (2.29–78.7%) were identified. A core microbiome could be found in leaf-associated endophytic communities in trees growing in different locations. This work demonstrates the application of Biolog EcoPlates in studies of the functional diversity of microbial communities in a niche other than soil and shows how it can be applied to the functional analyses of endomicrobiomes. This research can contribute to the popularisation of Biolog EcoPlates for the functional analysis of the endomicrobiome. This study confirms that the analysis of the structure and function of the plant endophytic microbiome plays a key role in the health control and the development of management strategies on bioenergy tree plantations.

Microbial functional diversity in rhizosphere and non-rhizosphere soil of different dominant species in a vegetation concrete slope

To investigate the effects of different dominant species on the microbial functional diversity of vegetation concrete substrates, the rhizosphere and non-rhizosphere soils of three dominant species (Pennisetum alopecuroides (PA), Arthraxon hispidus (AH) and Pueraria lobata (PL)) of vegetation concrete were studied using the Biolog-Eco method at Xiangjiaba Hydropower Station. The results showed that the microbial activity and microbial functional diversity indices in the rhizosphere soil of the three dominant plants were significantly higher than those in the non-rhizosphere soil and that the microbial activity and functional diversity indices in the rhizosphere and non-rhizosphere soil of AH, as well as in the rhizosphere soil of PL, were at a high level. The carbon sources predominantly used by rhizosphere soil microbes were carbohydrates, amino acids and polymers, while the carbon sources predominantly used by non-rhizosphere soil microbes were carboxylic acids, amino acids and polymers. The governing elements of the carbon source metabolic features of the microbial community were the soil moisture content (WC), organic matter (OM), total nitrogen (TN), potential of hydrogen (pH), microbial carbon (MBC), microbial nitrogen (MBN) and microbial phosphorus (MBP). Based on a thorough examination of these aspects, it was concluded that vegetation had altered the microbial community structure and functional diversity of the vegetation concrete substrate, perhaps improving the overall metabolic activity. A. hispidus with high adaptability should be prioritized in the regeneration of vegetation on concrete slopes.

Bacterial communities on polyethylene microplastics in mangrove ecosystems as a function of exposure sites: Compositions and ecological functions

Over the past decades, mangrove ecosystem has been polluted by plastic debris and microplastics (MPs) due to anthropogenic activities. Yet, little information is available on the composition and functional diversity of microbial communities on the surface of MPs in this ecosystem. The present study aims to investigate the bacterial communities growing on the surface of polyethylene microplastics (PE-MPs) in water, surface sediments and at the water-sediment interface (WSI) of mangrove ecosystems. Obtained results showed distinct variations in the taxonomic composition of bacterial communities among water, surface sediments and PE-MPs exposed to the different sites in mangrove ecosystems. For PE-MPs deployed to water, the dominant phyla were Proteobacteria and Bacteroidetes, accounting for 89.2% of the total abundance, while a relatively high proportion of Proteobacteria (85.6 ± 8.4%) was found for PE-MPs in sediments. For PE-MPs at the WSI, the top five phyla were Proteobacteria, Bacteroidetes, Planctomycetes, Actinobacteria and Firmicutes. Relatively abundant microorganisms on PE-MPs at the WSI were mainly due to tidal ebb and flood increasing interactions of sediment bacteria and PE-MPs. Functional annotation of prokaryotic taxa (FAPROTAX) analysis demonstrated that the ecological functions of microbial communities inhabiting PE-MPs were exposure site-dependent. Bacteria living on PE-MPs in water and at the WSI mainly participated in carbon and nitrogen cycle process, whereas PE-MPs in sediments enriched bacteria responsible for sulphur cycle. These results presented here highlight the importance of the exposure sites to MPs-associated bacteria in mangrove ecosystems.

Acetaminophen Levels Found in Recycled Wastewater Alter Soil Microbial Community Structure and Functional Diversity

The practice of using recycled wastewater (RWW) has been successfully adopted to address the growing demand for clean water. However, chemicals of emerging concern (CECs) including pharmaceutical products remain in the RWW even after additional cleaning. When RWW is used to irrigate crops or landscapes, these chemicals can enter these and adjacent environments. Unfortunately, the overall composition and concentrations of CECs found in different RWW sources vary, and even the same source can vary over time. Therefore, we selected one compound that is found frequently and in high concentrations in many RWW sources, acetaminophen (APAP), to use for our study. Using greenhouse grown eggplants treated with APAP concentrations within the ranges found in RWW effluents, we investigated the short-term impacts of APAP on the soil bacterial population under agricultural settings. Using Illumina sequencing-based approaches, we showed that APAP has the potential to cause shifts in the microbial community most likely by positively selecting for bacteria that are capable of metabolizing the breakdown products of APAP such as glycosides and carboxylic acids. Community-level physiological profiles of carbon metabolism were evaluated using Biolog EcoPlate as a proxy for community functions. The Biolog plates indicated that the metabolism of amines, amino acids, carbohydrates, carboxylic acids, and polymers was significantly higher in the presence of APAP. Abundance of microorganisms of importance to plant health and productivity was altered by APAP. Our results indicate that the soil microbial community and functions could be altered by APAP at concentrations found in RWW. Our findings contribute to the knowledge base needed to guide policies regulating RWW reuse in agriculture and also highlight the need to further investigate the effects of CECs found in RWW on soil microbiomes.

Soil Microbial Biomass and Functional Diversity of Microbial Communities in Native and Arable Soils of the Belogor’e Reserve

Soil Microbial Biomass and Functional Diversity of Microbial Communities in Native and Arable Soils of the Belogor’e Reserve

Metagenomic Views of Microbial Communities in Sand Sediments Associated with Coral Reefs.

Reef sediments, the home for microbes with high abundances, provide an important source of carbonates and nutrients for the growth and maintenance of coral reefs. However, there is a lack of systematic research on the composition of microbial community in sediments of different geographic sites and their potential effect on nutrient recycling and health of the coral reef ecosystem. In combination of biogeochemical measurements with gene- and genome-centric metagenomics, we assessed microbial community compositions and functional diversity, as well as profiles of antibiotic resistance genes in surface sediments of 16 coral reef sites at different depths from the Xisha islands in the South China Sea. Reef sediment microbiomes are diverse and novel at lower taxonomic ranks, dominated by Proteobacteria and Planctomycetota. Most reef sediment bacteria potentially participate in biogeochemical cycling via oxidizing various organic and inorganic compounds as energy sources. High abundances of Proteobacteria (mostly Rhizobiales and Woeseiales) are metabolically flexible and contain rhodopsin genes. Various classes of antibiotic resistance genes, hosted by diverse bacterial lineages, were identified to confer resistance to multidrug, aminoglycoside, and other antibiotics. Overall, our findings expanded the understanding of reef sediment microbial ecology and provided insights for their link to the coral reef ecosystem health.

Elevational Constraints on the Composition and Genomic Attributes of Microbial Communities in Antarctic Soils.

ABSTRACTThe inland soils found on the Antarctic continent represent one of the more challenging environments for microbial life on Earth. Nevertheless, Antarctic soils harbor unique bacterial and archaeal (prokaryotic) communities able to cope with extremely cold and dry conditions. These communities are not homogeneous, and the taxonomic composition and functional capabilities (genomic attributes) of these communities across environmental gradients remain largely undetermined. We analyzed the prokaryotic communities in soil samples collected from across the Shackleton Glacier region of Antarctica by coupling quantitative PCR, marker gene amplicon sequencing, and shotgun metagenomic sequencing. We found that elevation was the dominant factor explaining differences in the structures of the soil prokaryotic communities, with the drier and saltier soils found at higher elevations harboring less diverse communities and unique assemblages of cooccurring taxa. The higher-elevation soil communities also had lower maximum potential growth rates (as inferred from metagenome-based estimates of codon usage bias) and an overrepresentation of genes associated with trace gas metabolism. Together, these results highlight the utility of assessing community shifts across pronounced environmental gradients to improve our understanding of the microbial diversity found in Antarctic soils and the strategies used by soil microbes to persist at the limits of habitability.IMPORTANCE Antarctic soils represent an ideal system to study how environmental properties shape the taxonomic and functional diversity of microbial communities given the relatively low diversity of Antarctic soil microbial communities and the pronounced environmental gradients that occur across soils located in reasonable proximity to one another. Moreover, the challenging environmental conditions typical of most Antarctic soils present an opportunity to investigate the traits that allow soil microbes to persist in some of the most inhospitable habitats on Earth. We used cultivation-independent methods to study the bacterial and archaeal communities found in soil samples collected from across the Shackleton Glacier region of the Transantarctic Mountains. We show that those environmental characteristics associated with elevation have the greatest impact on the structure of these microbial communities, with the colder, drier, and saltier soils found at higher elevations sustaining less diverse communities that were distinct from those in more hospitable soils with respect to their composition, genomic attributes, and overall life-history strategies. Notably, the harsher conditions found in higher-elevation soils likely select for taxa with lower maximum potential growth rates and an increased reliance on trace gas metabolism to support growth.

两种镉积累型小麦根际微生物群落结构及功能多样性

PDF HTML阅读 XML下载 导出引用 引用提醒 两种镉积累型小麦根际微生物群落结构及功能多样性 DOI: 10.5846/stxb202104170997 作者: 作者单位: 作者简介: 通讯作者: 中图分类号: 基金项目: 安徽省自然科学基金项目（2008085MD120）；北京市农林科学院创新能力建设专项（KJCX20210439） Rhizosphere microbial community structure and functional diversity in two Cd-accumulating wheat cultivars Author: Affiliation: Fund Project: 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:为探究不同积累型小麦品种对根际微生物群落结构及功能多样性的影响，以镉低积累型小麦济麦22和镉高积累型小麦冀5265为研究材料，采用分离培养法和Biolog-Eco微平板法分析根际细菌数量、可培养优势群落结构以及微生物群落功能多样性。结果表明：污染土壤济麦22根际总细菌数量和抗Cd细菌数量均显著高于冀5265，而非污染土壤中两品种间无差异。污染土济麦22根际发现较多产脲酶和高镉抗性菌株（200 mg/L）。污染土济麦22根际优势菌多为Arthrobacter sp.和Bacillus sp.，冀5265根际优势菌主要为Streptomyces sp.；非污染土济麦22与冀5265根际优势菌群相似，均以Bacillus sp.为主。Biolog试验结果表明，两个小麦品种根际微生物群落对碳源的利用能力存在差异，济麦22根际微生物AWCD值、Mc Intosh指数、Shannon-Wiener指数、Simpson指数在污染土和无污染土中均显著高于冀5265。因此，污染土壤中不同积累型小麦品种根际微生物群落结构及功能多样性均存在差异，该研究结果对于揭示高低积累型小麦根际微生物机制提供了重要参考依据。 Abstract:In order to investigate the effects of the different accumulating wheat cultivars on rhizosphere microorganism community structure and functional diversity, low Cd-accumulating wheat Jimai 22 (JM22) and high Cd-accumulating wheat Ji 5265 (JI5265) were planted in pots filled with contaminated soil and non-contaminated soil and collected at the tillering stage of wheat. In total, four experimental treatments were set up, containing JM22 grown in contaminated soil (CJM), JI5265 grown in contaminated soil (CJI), JM22 grown in non-contaminated soil (NJM) and JI5265 grown in non-contaminated soil (NJI). The number of rhizosphere bacteria, community structure of culturable dominant bacteria and microbial community functional diversity were analyzed by traditional dilution plate culture method and Biolog-Eco microplate method. The results from the standard spread-plate method showed that the population of total bacteria and Cd-resistant bacteria in rhizosphere soil of JM22 were significantly higher than those of JI5265 in contaminated soil, but there was no significant difference in the population of total bacteria and Cd-resistant bacteria of rhizosphere soil between the two different accumulating wheat cultivars in non-contaminated soil. Studies on the biological characteristics of the isolated strains showed that more urease producing bacterial strains and Cd-resistant bacterial strains (200 mg/L) in rhizosphere soil of JM22 grown in contaminated soil were isolated than those of JI5265 grown in contaminated soil. Based on 16S rRNA gene sequences analysis, bacterial community composition was different in rhizosphere soil between cultivar JM22 and cultivar JI5265 in contaminated soil. Most of the dominant rhizosphere bacteria in JM22 were identified as Arthrobacter sp. and Bacillus sp., while Streptomyces sp. predominated in rhizosphere soil of wheat JI5265 in contaminated soil. The dominant rhizosphere bacteria in JM22 and JI5265 grown in non-contaminated soil were similar, and they were mainly Bacillus sp. The Biolog-Eco plate experiment results showed that there were differences in the utilization of carbon sources between the two wheat cultivars, and the average well color development (AWCD) values, Mc Intosh index, Shannon-Wiener index and Simpson index of rhizosphere microbes of wheat cultivar JM22 were significantly higher than those of cultivar JI5265 in both contaminated soil and non-contaminated soil after 120 h of incubation. Taken together, the community structure and functional diversity of rhizosphere microorganisms in the two Cd-accumulating wheat cultivars grown in contaminated soil were different. The results provide an important reference for understanding the rhizosphere microbial mechanism in high and low accumulating wheats. 参考文献 相似文献 引证文献

Responses of Soil Microbial Community Size, Respiration Rate and Functional Diversity to Invasive Plant Species Richness

Responses of Soil Microbial Community Size, Respiration Rate and Functional Diversity to Invasive Plant Species Richness

Diversity and function of microbial communities in the sand sheath of Agropyron cristatum by metagenomic analysis

The roots of most gramineous plants are surrounded by a variety of microorganisms; however, few studies have focused on the rhizosheath of psammophytes. Therefore, in this study, we used Illumina HiSeq high-throughput sequencing technology to analyse the composition and functional diversity of microbial communities in the rhizosheath of sand-grown Agropyron cristatum (L.) Gaertn. We found that the number of species and functions of microbial communities gradually decreased from the rhizosheath to the bulk soil. Thus, the microbial composition of the rhizosheath was richer and more diverse, and the abundance of bacteria, including Sphingosinicella, Rhizorhabdus, Friedmanniella, Geodermatophilus, Blastococcus, and Oscillatoria, was higher, and the abundance of fungi, such as Mycothermus, was higher. The abundance of CO2 fixation-related genes (acsA, Pcc, and cbbL) in the carbon cycle; NO3–, NO2–, NH2OH, and N2 transformation genes (nrtP, nirS, hao, and nifK) in the nitrogen cycle; soxB/A/C, Sat, and dsrB genes in the sulphur cycle; and 1-phosphate mannitol dehydrogenase (MtlD) gene and polyketide synthase gene (pks) were higher in the rhizosheath than in the bulk soil, as well as genes related to phosphorus uptake in the phosphorus cycle. Our findings showed that the rhizosheath may host the predominant microbial species related to the formation of a rhizosheath.

Taxonomical and functional diversity of microbial communities in two hot springs of the Baikal rift zone

The Baikal Rift Zone hosts many hot springs with a wide range of temperature and physical-chemical conditions, which may harbour different niches for the distribution of microbial communities. We investigated microbial community composition and their functional activity in two alkaline hot springs with a temperature range of 34.4 to 73.6°C. Comparative analysis of the composition of the dominant taxa showed significant differences depending on the collection sites. In the community of high-temperature zones with a water temperature of 55-64°C, a high proportion of thermophilic bacteria Acetothermia (up to 57.9%), Deinococcus-Thermus (up to 50%), and Aquificae (up to 10.8%). Proteobacteria (29-77%) and Firmicutes (15-26%) dominate in the sulphide-free Garga spring (73-75°C). The functional analysis of the microbial community showed that the primary producers are cyanobacteria, anoxygenic phototrophs, and chemolithotrophic bacteria. At the terminal stages of the mineralization of organic matter, sulphate-reducing bacteria are the main destructors in the microbial communities in hot springs. The cyano-bacterial and sulfidogenic microbial communities play an important role in the formation of geochemical barriers and mineral formation.

Response and oil degradation activities of a northeast Atlantic bacterial community to biogenic and synthetic surfactants

BackgroundBiosurfactants are naturally derived products that play a similar role to synthetic dispersants in oil spill response but are easily biodegradable and less toxic. Using a combination of analytical chemistry, 16S rRNA amplicon sequencing and simulation-based approaches, this study investigated the microbial community dynamics, ecological drivers, functional diversity and robustness, and oil biodegradation potential of a northeast Atlantic marine microbial community to crude oil when exposed to rhamnolipid or synthetic dispersant Finasol OSR52.ResultsPsychrophilic Colwellia and Oleispira dominated the community in both the rhamnolipid and Finasol OSR52 treatments initially but later community structure across treatments diverged significantly: Rhodobacteraceae and Vibrio dominated the Finasol-amended treatment, whereas Colwellia, Oleispira, and later Cycloclasticus and Alcanivorax, dominated the rhamnolipid-amended treatment. Key aromatic hydrocarbon-degrading bacteria, like Cycloclasticus, was not observed in the Finasol treatment but it was abundant in the oil-only and rhamnolipid-amended treatments. Overall, Finasol had a significant negative impact on the community diversity, weakened the taxa-functional robustness of the community, and caused a stronger environmental filtering, more so than oil-only and rhamnolipid-amended oil treatments. Rhamnolipid-amended and oil-only treatments had the highest functional diversity, however, the overall oil biodegradation was greater in the Finasol treatment, but aromatic biodegradation was highest in the rhamnolipid treatment.ConclusionOverall, the natural marine microbial community in the northeast Atlantic responded differently to crude oil dispersed with either synthetic or biogenic surfactants over time, but oil degradation was more enhanced by the synthetic dispersant. Collectively, our results advance the understanding of how rhamnolipid biosurfactants and synthetic dispersant Finasol affect the natural marine microbial community in the FSC, supporting their potential application in oil spills.43fSDwbdHYX3Ei4X1BHK1YVideo abstract

Profiling the microbial community structure and functional diversity of a dam‐regulated river undergoing gravel bar restoration

Abstract Comprehensive restoration programs are expected to influence sediment‐associated microbial community structure and functional diversity following changes attributed to the restoration of habitat characteristics in the dam‐impacted channel. To address if the construction or recreation of in‐channel structures, i.e., gravel bars, by implementing gravel augmentation and ecological flow restoration, resulted in habitat restoration and enhanced environmental heterogeneity, we profiled the community composition, estimated diversity, and annotated putative metabolic functions of the sediment microbial communities of the dam‐regulated Trinity River in northern California. Our results provided supporting evidence on the positive impact of habitat restoration conducted in the Trinity River with the non‐dam influenced, undisturbed tributaries as the basis of comparison. In addition, gravel bar recreation and restoration contributed to the increased microbial beta diversity, possibly through the increased environmental heterogeneity at the river scale. The significant positive correlation between the taxonomic and functional diversity of the identified microbial taxa suggests that differences in the detected putative metabolic functions were closely related to dissimilarities in community composition. We also provided valuable insights into the potential microbial processes in the sediment that might be contributing to the biogeochemical processes carried out by the microbial communities in the river. The results of this study have implications on the impact of construction and restoration of gravel bars in a dam‐impacted river on environmental heterogeneity and how this influences the taxonomic and functional diversities of sediment‐associated microbial communities.

Effect of round-shaped silver nanoparticles on the genetic and functional diversity of soil microbial community in soil and “soil-plant” systems

Silver and silver nanoparticles (AgNPs) are extensively used as antimicrobial agents in various products and consequently enter the soil ecosystem, in which they accumulate and can have adverse effects on above and belowground organisms. Since the composition of the soil microbiome could have a significant impact on soil fertility, we focused, in this study, on the effect of AgNPs on soil microbial communities. We evaluated the biomass, plant growth-promoting activities, and microbial genetic (taxonomical) and functional diversity in the soil and the “soil-plant” system using chemical, microbiological, and molecular biological methods, especially qPCR, RFLP, and REP-PCR. By compiling the results of the applied assays, we were able to correlate the changes in genetic diversity with the changes in functional diversity and their impact on the composition of soil organic matter. The effect of AgNPs was predominantly dose-dependent, whereas the concentration 100 mg kgdw−1 had the highest effect on all followed parameters. From the taxonomical point of view, AgNPs had the most significant impact on the relative abundance of Bacteroidetes, which increased in a dose-dependent manner, and Firmicutes, which decreased in a dose-dependent manner, and they caused the predominance of Ascomycota among Fungi. These changes in taxonomic diversity result in a significant decrease in the functional diversity of the microbial communities. Especially for the concentration 100 mg kgdw−1, we detected a significant decrease in the ability of the microbial community to utilize simple carbon substrates, determined by Biolog EcoPlates. We detected also a significant alteration in enzyme activity. The activity of enzymes responsible for depolymerization of complex organic matter was in a dose-dependent manner increased, whereas the highest activity reach samples amended with AgNPs at 100 mg kgdw−1. All these changes result in the accumulation of simple organic matter, which could increase osmotic pressure and have severe consequences on soil fertility. In amended soils, we detected alterations of activity of plant growth-promoting bacteria, specifically in the production of indole-3-acetic acid, 1-aminocyclopropane-1-carboxylic acid deaminase, and siderophores. All these activities are related to mitigating abiotic stress. The presence of plants in experimental soil had both a mitigating and deepening effect on the toxicity of AgNPs. Both effects probably relate to the influence of AgNPs on the selection of different microbial communities in the soil and the “soil-plant” system.

Functional diversity of microbial communities in inactive seafloor sulfide deposits.

The seafloor sulfide structures of inactive vents are known to host abundant and diverse microorganisms potentially supported by mineralogy of sulfides. However, little is known about the diversity and distribution of microbial functions. Here, we used genome-resolved metagenomics to predict microbial metabolic functions and the contribution of horizontal gene transfer to the functionality of microorganisms inhabiting several hydrothermally inactive seafloor deposits among globally distributed deep-sea vent fields. Despite of geographically distant vent fields, similar microbial community patterns were observed with the dominance of Gammaproteobacteria, Bacteroidota and previously overlooked Candidatus Patescibacteria. Metabolically flexible Gammaproteobacteria are major potential primary producers utilizing mainly sulfur, iron and hydrogen as electron donors coupled with oxygen and nitrate respiration for chemolithoautotrophic growth. In addition to heterotrophic microorganisms like free-living Bacteroidota, Ca. Patescibacteria potentially perform fermentative recycling of organic carbon. Finally, we provided evidence that many functional genes that are central to energy metabolism have been laterally transferred among members within the community and largely within the same class. Taken together, these findings shed light on microbial ecology and evolution in inactive seafloor sulfide deposits after the cessation of hydrothermal activities.