Microbial Characterization of Biological Filters Used for Drinking Water Treatment

The impact of preozonation and filter contact time (depth) on microbial communities was examined in drinking water biofilters treating Ohio River water which had undergone conventional treatment (coagulation, flocculation, sedimentation) or solutions of natural organic matter isolated from groundwater (both ozonated and nonozonated). With respect to filter depth, compared to filters treating nonozonated waters, preozonation of treated water led to greater differences in community phospholipid fatty acid (PLFA) profiles, utilization of sole carbon sources (Biolog), and arbitrarily primed PCR fingerprints. PLFA profiles indicated that there was a shift toward anaerobic bacteria in the communities found in the filter treating ozonated water compared to the communities found in the filter treating nonozonated settled water, which had a greater abundance of eukaryotic markers.     

The Relationships Among Disturbance, Substratum Size and Periphyton Community Structure

Numerous studies have determined the effects of physical disturbance on periphyton, however, the substrata used have varied in size among studies. In this study we examined the influence of substratum size on the change in periphyton exposed to three levels of disturbance. Periphyton communities were established in a large greenhouse tank on square unglazed tiles that were either 2.5, 5, or 7.5 cm on a side. Following community development sets of tiles were randomly assigned to controlled disturbances removing 25%, 50%, or 75% of the community or an undisturbed control. Following disturbance, changes in periphyton density were associated with both disturbance treatment and tile size as was taxa richness. Experimental results and direct observation revealed that algal growth was most concentrated along the edge of the tile and progressively declined toward the center. Thus, substratum size influences colonization and pre-disturbance community structure, which then affects the extent of periphyton community change due to different levels of disturbance.     

强化生物除磷系统的微生物种群及其表征技术

详细介绍了强化生物除磷系统(enhanced biological phosphate removal,简称EBPR)中的微生物种群及其表征技术,提出了研究EBPR中微生物种群及其表征技术的发展方向。     

Denitrification Performance and Microbial Community Structure of a Combined WLA–OBCO System

The contamination of surface water by nitrogen due to fertilizer application and discharge of wastewater is an increasingly serious problem. A multifunctional device, which combines water-lifting and aeration (WLA) with oligotrophic biological contact oxidation (OBCO), was developed for pretreatment of raw water to reduce nitrogen. The performance of nitrogen removal and changes in microbial community structure were investigated. The results showed that the combined technique of WLA-OBCO was feasible, and that ammonium, nitrate, total nitrogen and total organic carbon were effectively removed. Meanwhile, nitrite was mostly undetectable. The PCR-DGGE and clone sequencing results revealed that α-proteobacterium was the largest bacterial group, and Pseudomonas strains Y3 and J8 were the dominant bacteria.     

Microbial Diversity and Community Structure on Corroding Concretes

The objective of this study was to analyze bacterial diversity in two different concrete samples to understand the dominant types of bacteria that may contribute to concrete corrosion. Two concrete samples, HN-1 from the sunny side and HN-2 from dark and damp side, were collected from Zijin Mountain in Nanjing and genomic DNA was extracted. The partial bacterial 16S rRNA gene fragment was PCR amplified and two clone libraries were constructed. Amplified ribosomal DNA restriction analysis (ARDRA) was performed by digestion of the 16S rRNA gene and each unique restriction fragment polymorphism pattern was designated as an operational taxonomic unit (OTU). Phylogenetic trees of bacterial 16S rDNA nucleotide sequences were constructed. Sample HN-1 and HN-2 contained 21 OTUs and 26 OTUs, respectively. Proteobacteria and Planctomycetes were the predominant bacteria in both samples, and they are distributed among Herbaspirillum, Archangium, Phyllobacteriaceae and Planctomycetaceae. Cyanobacteria and Rubrobacter sp. are dominant in HN-1; while Acidobacteriaceae, Adhaeribacter sp. and Nitrospira sp. are predominant in HN-2. This distribution pattern was consistent with local environmental conditions of these two samples. The inferred physiological characteristics of these bacteria, based on relatedness of the DNA clone sequences to cultivated species, revealed different mechanisms of concrete corrosion depending on the local environmental conditions.     

二甲酸钾对白羽肉鸡生长性能和肠道菌群结构的影响

为评估二甲酸钾对畜禽肠道菌群的影响及其作为一种抗饲料添加剂的应用潜力,采用3日龄健康白羽肉鸡作为饲喂对象,在基础饲粮基础上添加质量浓度为0.1%、0.3%、0.5%、0.7%的二甲酸钾和含量为50 mg/mL的金霉素分别进行比较饲喂管理。记录28 d试验周期内白羽肉鸡的料重比变化,采集28 d时白羽肉鸡盲肠肠道内溶物,利用第三代测序技术对肠道菌群进行16S rDNA全长序列高通量测序。结果显示,饲喂0.3%的二甲酸钾能够显著降低料重比,对白羽肉鸡的生长性能具有明显的促进作用。饲喂0.3%的二甲酸钾对白羽肉鸡的肠道菌群结构造成了一定的影响,有效地提高了肠道菌群的物种多样性。优势菌群中,饲喂0.3%二甲酸钾与空白组相比,在门水平上,拟杆菌门相对丰度显著上升,厚壁菌门、变形菌门和Epsilonbacteraeota的相对丰度下降,产生了更有利于生长发育的微生物群落。同时,在属水平上,拟杆菌属相对丰度显著上升, Barnesiella和螺杆菌属的相对丰度下降,改善了肠道中微生物菌群的微生态健康。研究结果丰富了二甲酸钾和金霉素对白羽肉鸡生长性能和肠道菌群影响的认识,也为更全面了解二甲酸钾应用于替代抗生素对畜禽的影响提供了有价值的微生物学信息。     

The Impact of Biofumigation and Chemical Fumigation Methods on the Structure and Function of the Soil Microbial Community

Biofumigation (BIOF) is carried out mainly by the incorporation of brassica plant parts into the soil, and this fumigation activity has been linked to their high glucosinolate (GSL) content. GSLs are hydrolyzed by the endogenous enzyme myrosinase to release isothiocyanates (ITCs). A microcosm study was conducted to investigate the effects induced on the soil microbial community by the incorporation of broccoli residues into soil either with (BM) or without (B) added myrosinase and of chemical fumigation, either as soil application of 2-phenylethyl ITC (PITC) or metham sodium (MS). Soil microbial activity was evaluated by measuring fluorescein diacetate hydrolysis and soil respiration. Effects on the structure of the total microbial community were assessed by phospholipid fatty acid analysis, while the impact on important fungal (ascomycetes (ASC)) and bacterial (ammonia-oxidizing bacteria (AOB)) guilds was evaluated by denaturating gradient gel electrophoresis (DGGE). Overall, B, and to a lesser extent BM, stimulated microbial activity and biomass. The diminished effect of BM compared to B was particularly evident in fungi and Gram-negative bacteria and was attributed to rapid ITC release following the myrosinase treatment. PITC did not have a significant effect, whereas an inhibitory effect was observed in the MS-treated soil. DGGE analysis showed that the ASC community was temporarily altered by BIOF treatments and more persistently by the MS treatment, while the structure of the AOB community was not affected by the treatments. Cloning of the ASC community showed that MS application had a deleterious effect on potential plant pathogens like Fusarium, Nectria, and Cladosporium compared to BIOF treatments which did not appear to inhibit them. Our findings indicate that BIOF induces changes on the structure and function of the soil microbial community that are mostly related to microbial substrate availability changes derived from the soil amendment with fresh organic materials.     

Community Structure and Role Analysis in Biological Networks

Abstract

Complex network analysis has received increasing interest in recent years, which provides a remarkable tool to describe complex systems of interacting entities, particular for biological systems. In this paper, we propose a methodology for identifying the significant nodes of the networks, including core nodes, bridge nodes and high-influential nodes, based on the idea of community and two new ranking measures, InterRank and IntraRank. The results show the significant nodes form a small number in biological networks, and uncover the relative small number of which has advantage for reducing the dimensions of the network and possibly help to define new biological targets.     

固相反硝化系统中微生物群落结构的研究进展

固相反硝化是一种新型的异养反硝化工艺,采用固体有机物同时作为反硝化微生物的碳源和生物膜载体,可用于地下水和低C/N比污水的脱氮处理。固相反硝化系统生物膜的微生物群落结构决定固体碳源的降解效率,进而决定反硝化脱氮的速率和系统的稳定运行。因此,微生物群落结构的研究对于固相反硝化工艺的优化以及反应机理的解析具有重要意义。对不同固相反硝化系统微生物群落结构的研究现状和进展进行了综述,并探讨了当前研究中存在的问题和发展趋势。     

Microbial Community Structure in Three Deep-Sea Carbonate Crusts

Carbonate crusts in marine environments can act as sinks for carbon dioxide. Therefore, understanding carbonate crust formation could be important for understanding global warming. In the present study, the microbial communities of three carbonate crust samples from deep-sea mud volcanoes in the eastern Mediterranean were characterized by sequencing 16S ribosomal RNA (rRNA) genes amplified from DNA directly retrieved from the samples. In combination with the mineralogical composition of the crusts and lipid analyses, sequence data were used to assess the possible role of prokaryotes in crust formation. Collectively, the obtained data showed the presence of highly diverse communities, which were distinct in each of the carbonate crusts studied. Bacterial 16S rRNA gene sequences were found in all crusts and the majority was classified as α-, γ-, and δ- Proteobacteria. Interestingly, sequences of Proteobacteria related to Halomonas and Halovibrio sp., which can play an active role in carbonate mineral formation, were present in all crusts. Archaeal 16S rRNA gene sequences were retrieved from two of the crusts studied. Several of those were closely related to archaeal sequences of organisms that have previously been linked to the anaerobic oxidation of methane (AOM). However, the majority of archaeal sequences were not related to sequences of organisms known to be involved in AOM. In combination with the strongly negative δ ¹³C values of archaeal lipids, these results open the possibility that organisms with a role in AOM may be more diverse within the Archaea than previously suggested. Different communities found in the crusts could carry out similar processes that might play a role in carbonate crust formation.     

Impact of Dilution on Microbial Community Structure and Functional Potential: Comparison of Numerical Simulations and Batch Culture Experiments

A series of microcosm experiments was performed using serial dilutions of a sewage microbial community to inoculate a set of batch cultures in sterile sewage. After inoculation, the dilution-defined communities were allowed to regrow for several days and a number of community attributes were measured in the regrown assemblages. Based upon a set of numerical simulations, community structure was expected to differ along the dilution gradient; the greatest differences in structure were anticipated between the undiluted–low-dilution communities and the communities regrown from the very dilute (more than 10⁻⁴) inocula. Furthermore, some differences were expected among the lower-dilution treatments (e.g., between undiluted and 10⁻¹) depending upon the evenness of the original community. In general, each of the procedures used to examine the experimental community structures separated the communities into at least two, often three, distinct groups. The groupings were consistent with the simulated dilution of a mixture of organisms with a very uneven distribution. Significant differences in community structure were detected with genetic (amplified fragment length polymorphism and terminal restriction fragment length polymorphism), physiological (community level physiological profiling), and culture-based (colony morphology on R2A agar) measurements. Along with differences in community structure, differences in community size (acridine orange direct counting), composition (ratio of sewage medium counts to R2A counts, monitoring of each colony morphology across the treatments), and metabolic redundancy (i.e., generalist versus specialist) were also observed, suggesting that the differences in structure and diversity of communities maintained in the same environment can be manifested as differences in community organization and function.     

Community Structure and Biogeochemical Impacts of Microbial Life on Floating Pumice

Volcanic eruptions are a widespread force of geological and ecological disturbance and present recurrent opportunities for the study of biological responses to novel habitat formation. However, scientific study of such events is difficult given their short duration and often distant location. Here we report results from opportunistic sampling of unique volcano-generated habitats formed during the 2011 explosive eruption in the Puyehue-Cordón Caulle complex (Chile), when massive amounts of pumice were ejected, creating novel floating substrata that have never before been characterized from a microbiological perspective. DNA sequencing revealed a dynamic community of microbes that came to inhabit the pumice, with a unique composition distinct from that of the lakes'' surface waters and with suggestions of ecological convergence across lakes and sampling times. Furthermore, biogeochemical studies of net nutrient fluxes showed that, while the fresh pumice arriving to the lakes was an initial source of phosphorus (P), colonized pumice had high rates of nitrogen (N) and P uptake and was sufficiently abundant to represent a significant lake-wide nutrient sink. These findings highlight the remarkable versatility of microbes in exploiting novel environments and are consistent with a recent proposal of floating pumice as a favorable environment for the initial origins of life on early Earth.     

生物造粒流化床微生物落结构及其动态变化

为了研究生物造粒流化床污水处理反应器颗粒污泥中微生物群落结构及其动态变化,分别从生物造粒流化床10、60、110cm处取颗粒污泥,通过细胞裂解直接提取颗粒污泥细菌基因组DNA。以细菌和古细菌16S rRNA基因通用引物530F/1490R,对活性污泥中提取的细菌基因组DNA进行PCR扩增,长约1kb的PCR扩增产物纯化后经变性梯度凝胶电泳(DGGE)分离,获得微生物群落的DNA特征指纹图谱。结果显示,生物造粒流化床反应器颗粒污泥中的微生物群落非常丰富,在10cm处微生物的种属达到23种,60cm处为21种,110cm处为20种;生物造粒流化床不同高度都有一些各自的特有种属和共有种属,反应器不同高度的微生物群落演替不明显,微生物群落相似性为83.1%,群落结构较为稳定。     

生物造粒流化床微生物群落结构及其动态变化

为了研究生物适粒流化床污水处理反应器颗粒污泥中微生物群落结构及其动态变化,分别从生物造粒流化床10、60、110 cm处取颗粒污泥,通过细胞裂解直接提取颗粒污泥细菌基因组DNA.以细菌和古细菌16S rRNA基因通用引物530F/1490R,对活性污泥中提取的细菌基因组DNA进行PCR扩增,长约1 kb的PCR扩增产物纯化后经变性梯度凝胶电泳(DGGE)分离,获得微生物群落的DNA特征指纹图谱.结果显示,生物造粒流化床反应器颗粒污泥中的微生物群落非常丰富,在10 cm处微生物的种属达到23种,60 cm处为21种,110 cm处为20种;生物造粒流化床不同高度都有一些各自的特有种属和共有种属,反应器不同高度的微生物群落演替不明显,微生物群落相似性为83.1%,群落结构较为稳定.     

A Process Model to Evaluate the Performance of a Biological Aerated Filter

The biological aerated filter (BAF) is a three-phase reactor for waste water treatment that uses granular medium for biomass support. The parameter values from a process model for soluble COD were used to evaluate the impact of the medium characteristics and the process configuration on the performance of the BAF. In terms of reactor performance, the flow direction was more important than the medium characteristics. The results confirmed the applicability of the model.     

Microbial Community Structure and Denitrification in a Wetland Mitigation Bank

Wetland mitigation is implemented to replace ecosystem functions provided by wetlands; however, restoration efforts frequently fail to establish equivalent levels of ecosystem services. Delivery of microbially mediated ecosystem functions, such as denitrification, is influenced by both the structure and activity of the microbial community. The objective of this study was to compare the relationship between soil and vegetation factors and microbial community structure and function in restored and reference wetlands within a mitigation bank. Microbial community composition was assessed using terminal restriction fragment length polymorphism targeting the 16S rRNA gene (total bacteria) and the nosZ gene (denitrifiers). Comparisons of microbial function were based on potential denitrification rates. Bacterial community structures differed significantly between restored and reference wetlands; denitrifier community assemblages were similar among reference sites but highly variable among restored sites throughout the mitigation bank. Potential denitrification was highest in the reference wetland sites. These data demonstrate that wetland restoration efforts in this mitigation bank have not successfully restored denitrification and that differences in potential denitrification rates may be due to distinct microbial assemblages observed in restored and reference (natural) wetlands. Further, we have identified gradients in soil moisture and soil fertility that were associated with differences in microbial community structure. Microbial function was influenced by bacterial community composition and soil fertility. Identifying soil factors that are primary ecological drivers of soil bacterial communities, especially denitrifying populations, can potentially aid the development of predictive models for restoration of biogeochemical transformations and enhance the success of wetland restoration efforts.Wetlands provide more ecosystem services (e.g., flood control, water purification, nutrient cycling, and habitat for wildlife) per hectare than any other ecosystem (16). Riparian wetlands, in particular, are sites of intense biogeochemical activity and play an important role in improving water quality, recycling nutrients, and detoxifying chemicals (41). Changing patterns of land use over the last century have resulted in the loss of over half of the wetlands in the contiguous United States (17) and about 60% of wetlands in the Midwestern United States (82). The loss of ecosystem services through conversion of wetlands to alternative (primarily agricultural) land uses exacerbates nutrient pollution and eutrophication of downstream ecosystems (57). Declines in wetland acreage have continued despite a federal policy goal of no-net-loss of wetland acreage and function adopted in 1990 (7, 55). Wetland mitigation projects provide compensation for impacted wetlands and aim to replace the critical functions provided by wetlands. Despite decades of wetland mitigation, however, restoration efforts frequently fail to reestablish desired levels of ecosystem services. Restoration outcomes remain uncertain, and more information is necessary in order to improve monitoring and assessment of wetland development (13, 18, 50, 80).One approach to wetland compensation is through mitigation banks. These sites are areas that are restored, established, enhanced, or preserved for replacement of wetlands that will be affected by future land use change. Mitigation banks are considered “third-party” compensatory mitigation, where the permittee (e.g., developer planning to destroy a wetland) is responsible for purchasing wetland credits in acreage, but the wetland bank is established and managed by another party (24). Wetland mitigation banks have unique characteristics that distinguish them from smaller individual restoration projects (7, 69, 81). Due to their size, wetland mitigation banks are especially heterogeneous and may have a great deal of within-site variability in hydrology and nutrient status, making it challenging to implement a single restoration design. Thus, wetland mitigation banks require intense management and monitoring for improved success (7, 69, 81).Restoration efforts such as mitigation banks aim to replace chemical, physical, and biological ecosystem functions of wetlands that have been lost through anthropogenic disturbance (24). Monitoring of wetland mitigation sites has largely focused on measures of macro-scale community structure (e.g., vegetation surveys) (52) along with measures of hydrology and soil type (24). Measurement of vegetation is a common proxy for wetland performance but does not provide an accurate assessment of wetland function (6, 52). Quantitative assessment is achievable, however, for ecosystem services such as water quality improvement through nitrate removal, where well-characterized microbial mechanisms underlie denitrification processes.The link between microbial community structure and function in a restoration context is a topic of current interest (33). Relating microbial community composition and dynamics to chemical, physical, and biological variables can help to reveal important ecological drivers of microbial communities and their activities (26, 35, 42). Conserved bacterial functional genes related to specific biogeochemical transformations allow evaluation of the community structure of microbial populations directly involved in these processes (49, 60, 63, 77, 79). Assessing the diversity of microorganisms that are specifically involved in denitrification is possible through amplification of the nosZ gene, which encodes the catalytic subunit of nitrous oxide reductase, the enzyme responsible for the final step of denitrification (60, 63, 66). Phylogenetically diverse microorganisms can carry out denitrification though the majority of previously described denitrifiers belong to subphyla within the Proteobacteria (53, 56, 60, 61). Denitrification is a facultative process that occurs only under anaerobic conditions (53, 75). Complete denitrification to N₂ is more prevalent in anaerobic, saturated wetland ecosystems (14, 76), and incomplete denitrification to N₂O is the less desirable, more common endpoint of denitrification under more aerobic, drier conditions (14, 62). While the environmental factors (e.g., oxygen, carbon, nitrate, and pH) that influence bulk denitrification rates have been well characterized (31, 72), the influence of these factors on the composition of denitrifier communities, particularly in a restoration context, is unclear. Understanding the relationship between the microbial populations responsible for nitrogen transformations and easily measured environmental parameters (e.g., soil chemical and physical measures) could lead to assessment metrics that are linked directly to ecosystem functions such as denitrification and bridge the current gap in functional assessment methods (36, 60, 70).The objectives of this study were (i) to compare the microbial and plant community composition in restored wetlands to the composition in adjacent reference floodplain forest wetlands; (ii) to assess the relationship between microbial community composition (based on terminal restriction fragment length polymorphism [T-RFLP]) and potential denitrification activity throughout the mitigation bank; and (iii) to examine soil factors correlated with microbial community composition using both phylogenetic and functional gene markers. As soil environmental conditions affect microbial community structure and activity, we expected that sites where wetland hydrology and soil chemistry have been successfully restored would harbor microbial assemblages that are similar in composition and denitrification function to those observed in reference wetlands within this mitigation bank.     

克拉玛依石油污染土壤微生物群落结构及其代谢特征

为了分析克拉玛依油区内土壤中正构烷烃含量间的差异,微生物群落生理多样性、微生物代谢活性在不同石油污染梯度土壤中的变化规律。本研究采用GC、平板稀释法、Biolog微平板技术探讨了土壤微生物群落特征在3种不同污染程度下的变化情况。研究表明,石油污染土壤烷烃含量与微生物代谢活性呈显著负相关(r=-0.783, p<0.05)。随着石油污染程度增加微生物数量呈下降趋势,不同石油污染土壤中细菌数量占决定优势,细菌>真菌>放线菌。不同石油污染土壤微生物群落对6大碳源的利用体现出差异。主成分分析(PCA)表明,清洁土壤与石油污染土壤对底物利用有明显差异。石油污染严重土样碳源利用率为"酯类>酸类>胺类>氨基酸类>单糖/糖苷/聚合糖类>醇类"。本研究成果为后期修复污染土壤时调整投入的碳源底物等提供科学帮助。     

The Effect of Copper on The Structure of the Ammonia-Oxidizing Microbial Community in an Activated Sludge Wastewater Treatment Plant

Molecular approaches based on both whole-cell and extracted DNA were applied to assess chronic and acute effects of copper on the ammonia oxidizing bacteria (AOB) community in an activated sludge system. The ammonia monooxygenase amoA gene was chosen as the functional marker to evaluate changes in the AOB community. Using in situ polymerase chain reaction, we were able to visualize the peripheric distribution of the amoA gene-possessing bacteria in activated sludge flocs. The AOB biomass content was constant in both chronic and acute toxicity experiments, but the ammonia oxidizing activity, measured as ammonia uptake rate, was different. The AOB community structural changes due to the copper presence were evaluated by multivariate analysis of the DGGE bands profiles. The chronic contamination caused a change in the AOB community compared to the control. In contrast, acute inputs led to a temporary change in the AOB community, after which the community was similar to the control. Recovery after acute intoxication was achieved after 72 h. The present study reports on the effects of chronic and acute copper contamination on the ammonia uptake ability of the AO microorganisms and the structure of the AOB community in a wastewater system and, as a consequence, gives indications on the response of wastewater plants under similar conditions.     

Impact of Oil on Bacterial Community Structure in Bioturbated Sediments

Oil spills threaten coastlines where biological processes supply essential ecosystem services. Therefore, it is crucial to understand how oil influences the microbial communities in sediments that play key roles in ecosystem functioning. Ecosystems such as sediments are characterized by intensive bioturbation due to burrowing macrofauna that may modify the microbial metabolisms. It is thus essential to consider the bioturbation when determining the impact of oil on microbial communities. In this study, an experimental laboratory device maintaining pristine collected mudflat sediments in microcosms closer to true environmental conditions – with tidal cycles and natural seawater – was used to simulate an oil spill under bioturbation conditions. Different conditions were applied to the microcosms including an addition of: standardized oil (Blend Arabian Light crude oil, 25.6 mg.g⁻¹ wet sediment), the common burrowing organism Hediste (Nereis) diversicolor and both the oil and H. diversicolor. The addition of H. diversicolor and its associated bioturbation did not affect the removal of petroleum hydrocarbons. After 270 days, 60% of hydrocarbons had been removed in all microcosms irrespective of the H. diversicolor addition. However, 16S-rRNA gene and 16S-cDNA T-RFLP and RT-PCR-amplicon libraries analysis showed an effect of the condition on the bacterial community structure, composition, and dynamics, supported by PerMANOVA analysis. The 16S-cDNA libraries from microcosms where H. diversicolor was added (oiled and un-oiled) showed a marked dominance of sequences related to Gammaproteobacteria. However, in the oiled-library sequences associated to Deltaproteobacteria and Bacteroidetes were also highly represented. The 16S-cDNA libraries from oiled-microcosms (with and without H. diversicolor addition) revealed two distinct microbial communities characterized by different phylotypes associated to known hydrocarbonoclastic bacteria and dominated by Gammaproteobacteria and Deltaproteobacteria. In the oiled-microcosms, the addition of H. diversicolor reduced the phylotype-richness, sequences associated to Actinobacteria, Firmicutes and Plantomycetes were not detected. These observations highlight the influence of the bioturbation on the bacterial community structure without affecting the biodegradation capacities.     

Investigating the Impact of Storage Conditions on Microbial Community Composition in Soil Samples

Recent advances in DNA sequencing technologies have allowed scientists to probe increasingly complex biological systems, including the diversity of bacteria in the environment. However, despite a multitude of recent studies incorporating these methods, many questions regarding how environmental samples should be collected and stored still persist. Here, we assess the impact of different soil storage conditions on microbial community composition using Illumina-based 16S rRNA V4 amplicon sequencing. Both storage time and temperature affected bacterial community composition and structure. Frozen samples maintained the highest alpha diversity and differed least in beta diversity, suggesting the utility of cold storage for maintaining consistent communities. Samples stored for intermediate times (three and seven days) had both the highest alpha diversity and the largest differences in overall beta diversity, showing the degree of community change after sample collection. These divergences notwithstanding, differences in neither storage time nor storage temperature substantially altered overall communities relative to more than 500 previously examined soil samples. These results systematically support previous studies and stress the importance of methodological consistency for accurate characterization and comparison of soil microbiological assemblages.