Bacterial diversity in ferruginous duricrust (canga) and the physicochemical variables affecting their prevalence, distribution and predicted metabolic pathways.

Soil microorganisms, crucial players of soil organic matter degradation, contribute substantially to global carbon and nitrogen biogeochemical cycles. Although microbial community structure and diversity have been extensively studied at different latitudes worldwide, the relationship between microbial communities, environmental drivers, and ecosystem functions across latitudes has yet to be explored. Here we investigate soil bacterial and fungal community structure and diversity, and ecosystem multifunctionality across different biomes of the European continent from southern Spain (37°N) to Sweden (60°N). Bacterial alpha-diversity increased with increasing the latitude, while fungal alpha-diversity showed an opposite pattern. Fungal communities were more geographically dispersed than bacterial communities. Microbial communities were structured by soil temperature, water content, and resources (TOC, C/N ratio and phosphate). While multifunctionality index related to N cycling functions decreased linearly and significantly with increasing bacterial diversity, it increased significantly with the increases in fungal diversity indices. Our study sheds light on the soil microbial complexity, microbial diversity and function relationship across latitudes and biomes, and highlights the importance of microbial diversity and community structure in driving soil multifunctionality.

Effects of land-use conversion from paddy field to orchard farm on soil microbial genetic diversity and community structure

Microbial communities play crucial roles in the biogeochemical cycling of many important soil elements. Pesticides are known to affect non-targeted soil microorganisms. Glyphosate (GP) and diquat (DQ), two commonly used non-selective herbicides, often co-exist in lateritic paddy soil rich in iron/aluminum oxides. However, there is limited information on their co-impact on microbial community structure and diversity in this type of soil. Here, the short-term effects of combined exposure to GP and DQ on microbial diversity and community structure shifts were investigated in lateritic paddy soil from a tropical agricultural region (Hainan, China). The combined utilization dosages of two herbicides were set in three concentrations: low concentration (1 fold of the recommended dosage), medium concentration (10 fold of the recommended dosage) and high concentration (100 fold of the recommended dosage). The structure and diversity of microbial communities were determined via 16S rRNA and ITS gene high-throughput sequencing. The results revealed that Actinobacteria and Proteobacteria were the most sensitive microbial phyla to the combined exposure of GP and DQ in lateritic paddy soil. The combined exposure to GP and DQ increased the abundance of Actinobacteria but significantly inhibited that of Proteobacteria, especially at low and medium concentrations. Compared with CK, mixed herbicide (GP + DQ) had no adverse effects on the richness of bacteria and fungi communities as well as on the diversity of bacteria communities, but it significantly decreased the diversity of fungi communities at high concentrations within 28 days. However, the effects of combined exposure to GP and DQ on soil microbial richness and diversity were not significantly different from those of separate exposure of the two herbicides. In conclusion, the combined application of GP and DQ had no more adverse effects on soil microorganisms. Therefore, these two herbicides can be used reasonably in actual agricultural production.

Microbial communities composed of bacteria, archaea and fungi play a pivotal role in driving the biogeochemical cycles in the marine ecosystem. Despite the vastness of the South Indian Ocean, only a few studies reported the simultaneous analysis of bacterial, archaeal and fungal diversity therein, particularly archaeal and fungal communities in deep-sea environments received less attention previously. In this study, microbial diversity, community composition and dynamics in microbial community structure in eight deep-sea sediment samples collected from different sites at varying depths of the South Indian Ocean were explored using Next-Generation Sequencing. In total, 21 bacterial phyla representing 541 OTUs were identified from the eight samples, where phylum Proteobacteria was found as the most abundant bacterial phylum in five out of eight samples. Firmicutes and Chloroflexi were the dominant phyla in the rest of the three samples. In the case of archaea, uncultured species belonging to the phyla Thaumarchaeota and Euryarchaeota were the abundant taxa in all the samples. Similarly, Ascomycota and Basidiomycota were the most abundant fungal phyla present therein. In all the eight samples studied here, about 10-58% and 19-26% OTUs in archaeal and fungal communities were mapped to unclassified taxa respectively, suggesting the lack of representation in databases. Co-occurrence network analysis further revealed that bacterial communities tend to be more dynamic than archaeal and fungal communities. This study provides interesting insights into the microbial diversity, community composition and dynamics in microbial community structure in the deep-sea sediments of the South Indian Ocean.

High-throughput 16S rRNA and 18S rRNA sequencing were performed to study the changes of soil microbial diversity and community structure under different heavy metal pollution levels in Chengxian lead-zinc mining area, Gansu Province. In this study, we characterized the main physicochemical properties, multiple heavy metal pollution, and microbial community structure of the soil in the tailings. The results show that the soil near the tailings pond was alkaline, barren and the heavy metals were seriously polluted. The microbial diversity and richness of S1 and S2 sites were significantly lower than that of CK2 site (P<0·05), indicating that the heavy metal pollution could change the physicochemical properties and microbial community structure in soil. Among 97 identified core operating taxa of fungal communities, Ascomycota, Teguta and Basidiomycota were dominant at the phylum level, while among 1523 identified core operating taxa of bacterial communities, Actinomycota was dominant at the phylum level. In addition, the redundancy analysis and Spearman correlation analysis showed that the physicochemical properties and the heavy metal concentration had significant effects on the composition and distribution of soil microbial community. The basic characteristics of soil physicochemical properties, multiple heavy metal pollution and microbial community structure in the tailings were revealed, hoping to provide a basis for ecological rehabilitation of tailings by revealing the variance rule of microbial community diversity in the future.

Microbial communities are key components of lake ecosystems and play central roles in lake biogeochemical cycles. Freshwater lakes, in turn, have a disproportionate influence on global carbon and nitrogen cycling, while also acting as 'sentinels' of environmental change. Determining what factors regulate microbial community dynamics and their relationship to lake biogeochemistry is therefore essential to understanding global change feedbacks. We used Illumina sequencing of >2 million 16S rRNA genes to examine microbial community structure and diversity in relation to spatial, temporal and biogeochemical variation, within and across lakes located along a 871 m elevation gradient in Yosemite National Park, California, USA. We captured a rich microbial community that included many rare operational taxonomic units (OTUs), but was dominated by a few bacterial classes and OTUs frequently detected in other freshwater ecosystems. Neither richness, evenness nor overall diversity was directly related to elevation. However, redundancy analysis showed that changes in microbial community structure were significantly related to elevation. Along with sampling period and dissolved nutrient concentrations, 29% of the variation in community structure could be explained by measured variables - in congruence with studies in other lakes using different techniques. We also found a distance-decay relationship in microbial community structure across lakes, suggesting that both local environmental factors and dispersal play a role in structuring communities.

The living soil system is of primary importance in sustainable agricultural production. Soil quality is considered as an integrative indicator of environmental quality, food security and economic viability. Therefore, soil itself serves as a potential indicator for monitoring sustainable land management. As part of the soil quality concept, a healthy soil supports high levels of biological diversity, activity, internal nutrient cycling and resilience to disturbance. The use of microbial community structure and diversity as an indicator to monitor soil quality is challenging due to little understanding of the relationship between community structure and soil function. This review addresses two critical questions regarding soil quality: (1) which soil microbial properties, particularly diversity and community structure, most effectively characterize soil quality and can be used as indicators, and (2) how can soil quality assessed by such indicators be improved or maintained?We provide an overview of available techniques to characterize microbial community structure and diversity, and furnish information pertaining to strategies that can improve microbial diversity, including mycorrhizae, in relation to soil quality by adopting suitable agricultural practices to sustain soil and crop productivity. These techniques include those for structural profiling, i.e. fatty acid methyl ester analysis, genetic profiling, i.e. PCR-DGGE, SSCP, T-RFLP, functional profiling, i.e. catabolic profiling, diversity of enzyme activity, and to profile both structural and functional communities comprehensively, i.e. gene chip. We identify the importance of minimum data sets (MDS) of microbial indicators, such that they must be (i) compatible with basic ecosystem processes in soil as well as physical or chemical indicators of soil health, (ii) sensitive to management in acceptable time frames, (iii) easy to assess or measure, (iv) composed of robust methodology with standardized sampling techniques, (v) cost-effective, and (vi) relevant to human goals, food security, agricultural production, sustainability and economic efficiency. We focus on specific agricultural strategies such as tillage, crop rotations, organic amendments and microbial inoculation to improve soil quality by managing microbial communities and diversity. Overall, we provide techniques to assess microbial communities and diversity, and their management through agricultural practices to improve quality of soil.KeywordsSoil qualityMicrobial communityDiversityGene chipAMFMDSTillageCrop rotationInoculation

Globally nitrogen addition alters soil microbial community structure, but has minor effects on soil microbial diversity and richness

Chemical composition of soil carbon is governed by microbial diversity during understory fern removal in subtropical pine forests

Soil salinization is one main environmental factor restricting plant growth and agricultural productivity. However, phytoremediation is one of the important means to improve saline-alkali soil by planting halophytes or salt-tolerant plants. In order to study whether there are differences among soil microorganisms in different phytoremediation, the effects of four plants, including alfalfa (MX), oil sunflower (YK), maize (YM) and ryegrass (HMC) on soil physicochemical properties, enzyme activity and microbial community diversity and composition were investigated in this study and the relationships between microbial community structure and soil physicochemical properties, enzyme activity were analyzed. The results showed that all plants treatments significantly decreased pH, TS (total saltinity) and BD (bulk density), while increased OM (organic matter), TN (total nitrogen), AN (available nitrogen), TP (total phosphorus), AP (available phosphorus), TK (total potassium) and TPOR (total porosity), and the number of nitrite bacteria reduced by planting at the same time. Except for YM, other treatments significantly increased the number of nitrifying and denitrifying bacteria compared with CK, while only YK increased that of fungi. Additionally, all plants increased the activity of nitrite reductase and decreased that of urease. More interestingly, plants treatments shifted microbial community compositions, and only YM significantly decreased the bacterial diversity and increased the fungal diversity. Redundancy analysis suggested that TK, pH, BD, TS, AN, OM and nitrite reductase, lignin peroxidase were the key environmental factors that shaped the bacterial community structure, while that of fungi was mainly driven by OM, nitrite reductase, urease and lignin peroxidase. The results indicated that MX and YM are the best choice for remediation of saline-alkali soil. These data can provide certain theoretical basis for the further restoration of saline-alkali land. HIGHLIGHTS The effects of different phytoremediation on microbial diversity and community structure were different. Phytoremediation can significantly decreased pH, TS and BD, while increased OM, TN, AN, TP, AP, TK and TPOR in saline-alkali soil. All plants increased the activity of nitrite reductase and decreased the activity of urease.

Lonar Lake is a hypersaline and hyperalkaline soda lake and the only meteorite impact crater in the world situated in basalt rocks. Although culture-dependent studies have been reported, a comprehensive understanding of microbial community composition and structure in Lonar Lake remains elusive. In the present study, microbial community structure associated with Lonar Lake sediment and water samples was investigated using high-throughput sequencing. Microbial diversity analysis revealed the existence of diverse, yet largely consistent communities. Proteobacteria (30%), Actinobacteria (24%), Firmicutes (11%), and Cyanobacteria (5%) predominated in the sequencing survey, whereas Bacteroidetes (1.12%), BD1-5 (0.5%), Nitrospirae (0.41%), and Verrucomicrobia (0.28%) were detected in relatively minor abundances in the Lonar Lake ecosystem. Within the Proteobacteria phylum, the Gammaproteobacteria represented the most abundantly detected class (21–47%) within sediment samples, but only a minor population in the water samples. Proteobacteria and Firmicutes were found at significantly higher abundance (p ≥ 0.05) in sediment samples, whereas members of Actinobacteria, Candidate division TM7 and Cyanobacteria (p ≥ 0.05) were significantly abundant in water samples. Compared to the microbial communities of other hypersaline soda lakes, those of Lonar Lake formed a distinct cluster, suggesting a different microbial community composition and structure. Here we report for the first time, the difference in composition of indigenous microbial communities between the sediment and water samples of Lonar Lake. An improved census of microbial community structure in this Lake ecosystem provides a foundation for exploring microbial biogeochemical cycling and microbial function in hypersaline lake environments.

Context Gastrointestinal microorganisms play an important role in ruminant digestion and metabolism, immune regulation and disease prevention and control. Different parts of the digestive tract have different functions and microbial community structures. Aims This study aims to explore the microbial diversity in the rumen and the small intestine of Xinong Saanen dairy goats. Methods Rumen fluid and jejunum fluid from three Xinong Saanen dairy bucks with the average slaughter weight of 33.93 ± 0.68 kg were collected and analysed for microbial diversity, by using 16S rRNA gene high-throughput sequencing. Key results In total, 1118 operational taxonomic units (OTUs) were identified, with 1020 OTUs and 649 OTUs being clustered to rumen and jejunum samples respectively. Alpha-diversity indices were significantly (P &lt; 0.05) different between rumen and jejunum, as indicated by the fact that the rumen microbial community diversity, richness and uniformity/evenness were higher than those of jejunum. At the phylum level, the dominant phyla in the rumen were Bacteroidetes (66.7%) and Firmicutes (25.1%), accounting for 91.8% of the rumen microorganisms. The dominant phylum in the jejunum was Firmicutes, accounting for 73.0% of the jejunum microorganisms. At the genus level, the dominant bacteria in the rumen were Prevotella_1, norank_f_Bacteroidales_BS11_gut_group, Rikenellaceae_RC9_gut_group, Christensenellaceae_R-7_group and Family_XIII_AD3011_group, whereas the dominant bacteria in the jejunum were Omboutsia, Aeriscardovia, Intestinibacter, unclassified_f_Peptostreptococcaceae and unclassified_f_Bifidobacteriaceae. Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) results showed that the major functions of microorganisms in the rumen and jejunum were carbohydrate metabolism, amino acid metabolism, nucleotide metabolism, membrane transport and translation. Interestingly, fructose and mannose metabolism and peptidoglycan biosynthesis were abundant in the rumen, while homologous recombination and nucleotide excision repair were abundant in the jejunum. Conclusions Our study clarified the differences in microbial diversity and community structure between the rumen and the jejunum in Xinong Saanen dairy goats. Prevotella was the most predominant genus in the rumen, compared with Romboutsia, Bifidobacterium as well as Peptostreptococcaceae genera, which were the predominant genera in the jejunum. Implications In combination with the functional prediction of microorganisms and the metabolic characteristics of different parts of the digestive tract in ruminants, our findings provided information for further exploring the relationship among genes, species and functions of microorganisms and their hosts’ nutritional and physiological functions.

The combination technique of pre-ozonation and bioaugmentation is promising for remediating benzo[a]pyrene (BaP)-contaminated soil. However, little is known about the effect of coupling remediation on the soil biotoxicity, soil respiration, enzyme activity, microbial community structure, and microbial in the process of remediation. This study developed two coupling remediation strategies (pre-ozonation coupled with bioaugmentation by addition of polycyclic aromatic hydrocarbons (PAHs) specific degrading bacteria or activated sludge), compared with sole ozonation and sole bioaugmentation, to improve degradation of BaP and recovery of soil microbial activity and community structure. Results showed that the higher removal efficiency of BaP (92.69-93.19%) was found in coupling remediation, compared with sole bioaugmentation (17.71-23.28%). Meanwhile, coupling remediation significantly reduced the soil biological toxicity, promoted the rebound of microbial counts and activity, and recovered the species numbers and microbial community diversity, compared with sole ozonation and sole bioaugmentation. Besides, it was feasible to replace microbial screening with activated sludge, and coupling remediation by addition of activated sludge was more conducive to the recovery of soil microbial communities and diversity. This work provides a strategy of pre-ozonation coupled with bioaugmentation to further degrade BaP in soil by promoting the rebound of microbial counts and activity, as well as the recovery of species numbers and microbial community diversity.

AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 55:81-93 (2009) - DOI: https://doi.org/10.3354/ame01283 Influence of allochthonous matter on microbial community structure and function in an upwelling system off the northwest Iberian Peninsula Eva Teira*, María Aranguren-Gassis, Jose González, Sandra Martínez-García, Patricia Pérez, Pablo Serret Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, Campus Lagoas-Marcosende, 36310 Vigo, Spain *Email: teira@uvigo.es ABSTRACT: The input of allochthonous matter of continental origin to coastal zones globally may cause changes in the activity (function) as well as the taxonomic composition (structure) of the microbial plankton community. The goal of the present study was the simultaneous analysis of microbial plankton community structure (size-fractionated phytoplankton biomass, bacterial community composition) and function (particulate and dissolved primary production, bacterial production, microbial plankton community respiration) in the northwest Iberian coastal transition zone during a dry (February 2005) and a rainy (October 2005) period. An influence of freshwater input was observed in October, even at an offshore site, but not in February. We found an autotrophic community dominated by picophytoplankton during both sampling periods. In contrast, the bacterial groups Beta- and Gammaproteobacteria were significantly more abundant during the high precipitation period. Primary production rates were low and similar during both sampling periods; however, bacterial production was 8-fold and community respiration was 3-fold higher in October than in February. Consequently, the microbial community metabolism was net autotrophic in February and net heterotrophic in October. The high precipitation and the significant presence of bacteria belonging to the Betaproteobacteria, typical for freshwater systems, in October compared to February, strongly suggest an influence of material of continental origin on microbial metabolism in this coastal transition zone. KEY WORDS: Microbial plankton structure · Primary production · Bacterial production · Respiration · Allochthonous matter · NW Iberian Peninsula Full text in pdf format PreviousNextCite this article as: Teira E, Aranguren-Gassis M, González J, Martínez-García S, Pérez P, Serret P (2009) Influence of allochthonous matter on microbial community structure and function in an upwelling system off the northwest Iberian Peninsula. Aquat Microb Ecol 55:81-93. https://doi.org/10.3354/ame01283 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 55, No. 1. Online publication date: April 06, 2009 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2009 Inter-Research.

Summary Resource control over abundance, structure and functional diversity of soil microbial communities is a key determinant of soil processes and related ecosystem functioning. Copiotrophic organisms tend to be found in environments which are rich in nutrients, particularly carbon, in contrast to oligotrophs, which survive in much lower carbon concentrations. We hypothesized that microbial biomass, activity and community structure in nutrient‐poor soils of an Amazonian rain forest are limited by multiple elements in interaction. We tested this hypothesis with a fertilization experiment by adding C (as cellulose), N (as urea) and P (as phosphate) in all possible combinations to a total of 40 plots of an undisturbed tropical forest in French Guiana. After 2 years of fertilization, we measured a 47% higher biomass, a 21% increase in substrate‐induced respiration rate and a 5‐fold higher rate of decomposition of cellulose paper discs of soil microbial communities that grew in P‐fertilized plots compared to plots without P fertilization. These responses were amplified with a simultaneous C fertilization suggesting P and C colimitation of soil micro‐organisms at our study site. Moreover, P fertilization modified microbial community structure (PLFAs) to a more copiotrophic bacterial community indicated by a significant decrease in the Gram‐positive : Gram‐negative ratio. The Fungi : Bacteria ratio increased in N fertilized plots, suggesting that fungi are relatively more limited by N than bacteria. Changes in microbial community structure did not affect rates of general processes such as glucose mineralization and cellulose paper decomposition. In contrast, community level physiological profiles under P fertilization combined with either C or N fertilization or both differed strongly from all other treatments, indicating functionally different microbial communities. While P appears to be the most critical from the three major elements we manipulated, the strongest effects were observed in combination with either supplementary C or N addition in support of multiple element control on soil microbial functioning and community structure. We conclude that the soil microbial community in the studied tropical rain forest and the processes it drives is finely tuned by the relative availability in C, N and P. Any shifts in the relative abundance of these key elements may affect spatial and temporal heterogeneity in microbial community structure, their associated functions and the dynamics of C and nutrients in tropical ecosystems.