Effect of the diverse combinations of useful microbes and chemical fertilizers on important traits of potato

The belowground soil environment is an active space for microbes, particularly Arbuscular Mycorrhizal Fungi (AMF) and P hosphate Solubilizing Bacteria (PSB) that can colonize with roots of higher plants. In the present experiment, we evaluated the combination of microbial inoculants with the different doses of urea and superphosphate in a complete randomized block design (CRBD). Three different doses of urea and superphosphate were tested, i.e., recommended dose, 75% of the recommended dose and 125% of the recommended dose, independently and in combination with three microbial groups viz. Glomus mosseae (AMF), Bacillus subtilis (PSB) and Nitrifying microorganisms (Nitrosomonas + Nitrobacter, NN). Overall, there were 16 treatment combinations used, and studied the number of tubers per plant, the weight of tubers, moisture content, and the number of nodes per tubers which were best in treatment comprising of AMF + PSB + NN + 75% of urea + superphosphate. From our results, it is suggested for the growers to use a lesser quantity of fertilizers from the recommended dose along with some bioinoculants to maintain the soil fertility and also to achieve the yield targets by decreasing the cost of chemical fertilizers.     

Isolation and Identification of Lead (Pb) Solubilizing Bacteria from Automobile Waste and Its Potential for Recovery of Lead from End of Life Waste Batteries

Abstract

End of life waste Lead (Pb) acid batteries are one of the largest sources of secondary lead production globally. Recycling lead by melting down used batteries is a commercial trade all over the world; but, regrettably, reprocessing lead from end of life batteries is reported for anthropogenic lead exposures causing harsh human health consequence and environmental pollution. The current research intends to isolate and identify Lead (Pb) solubilizing bacteria from automobile waste deposits from Agartala city in Tripura state of India. Scanning Electron Microscope equipped with energy-dispersive X-ray characterization of the grounded lead sample was carried out, and the micrographs demonstrated scattered structures across the matrix. The X-ray diffraction (XRD) spectrum indicates the presence of Lead Oxide (PbO), Lead dioxide (PbO₂), and Lead sulfate (PbSO₄) in the collected samples. A single bacterium viewing observable growth on Pb supplemented plates was isolated and its Pb recovering capability was estimated through ICP AES analysis. Molecular characterization of the bacterium was investigated using 16S rRNA sequencing along with isolated culture was taxonomically grouped as Cupriavidus sp. The genomic DNA sequences were submitted in NCBI GenBank with the accession number MG171197. In the present case of inspection, the ability of the bacterial strain to recover Pb from end life battery waste was carried out in laboratory scale on a shake flask for 20?days. The experiment conducted under optimum bioleaching parameters with initial pH 6, 5% w/v of microbial culture, 2% pulp density and 2?g/100?mL dextrose concentration at 30?°C temperature with a speed of 200?RPM resulted in 67% Pb recovery from the battery sample. This investigation emphasizes the significance of Pb recycling ability of native bacterial isolate for efficient Pb bio-recovery from end of life waste batteries.     

An evaluation of biofilm development utilizing non‐destructive attenuated total reflectance Fourier transform infrared spectroscopy

Chemical changes that occur within a microbial biofilm during development on a germanium internal reflection element (IRE) were monitored by attenuated total reflection Fourier transform infrared spec‐troscopy (ATR/FT‐IR) for 188 h. The amount of protein detected at the IRE/medium interface increased throughout the course of the experiment. Extracellular polysaccharides were mainly produced during the initial stages of biofilm development. These results demonstrate that changes in metabolic activity of surface‐associated bacteria during biofilm development on surfaces exposed to a flowing bulk aqueous phase can be evaluated by ATR/FT‐IR.     

Microbial acetyl-CoA metabolism and metabolic engineering

Recent concerns over the sustainability of petrochemical-based processes for production of desired chemicals have fueled research into alternative modes of production. Metabolic engineering of microbial cell factories such as Saccharomyces cerevisiae and Escherichia coli offers a sustainable and flexible alternative for the production of various molecules. Acetyl-CoA is a key molecule in microbial central carbon metabolism and is involved in a variety of cellular processes. In addition, it functions as a precursor for many molecules of biotechnological relevance. Therefore, much interest exists in engineering the metabolism around the acetyl-CoA pools in cells in order to increase product titers. Here we provide an overview of the acetyl-CoA metabolism in eukaryotic and prokaryotic microbes (with a focus on S. cerevisiae and E. coli), with an emphasis on reactions involved in the production and consumption of acetyl-CoA. In addition, we review various strategies that have been used to increase acetyl-CoA production in these microbes.     

A yeast co-culture-based biosensor for determination of waste water contamination levels

Artificial microbial co-cultures were formed to develop the receptor element of a biosensor for assessment of biological oxygen demand (BOD). The co-cultures possessed broad substrate specificities and enabled assays of water and fermentation products within a broad BOD range (2.4–80 mg/dm³) with a high correlation to the standard method (R = 0.9988). The use of the co-cultures of the yeasts Pichia angusta, Arxula adeninivorans and Debaryomyces hansenii immobilized in N-vinylpyrrolidone-modified poly(vinyl alcohol) enabled developing a BOD biosensor possessing the characteristics not inferior to those in the known biosensors. The results are indicative of a potential of using these co-cultures as the receptor element base in prototype models of instruments for broad application.     

L-Asparaginase: A Promising Chemotherapeutic Agent

ABSTRACT

This article comprises detailed information about L-asparaginase, encompassing topics such as microbial and plant sources of L-asparaginase, treatment with L-asparaginase, mechanism of action of L-asparaginase, production, purification, properties, expression and characteristics of l-asparaginase along with information about studies on the structure of L-asparaginase. Although L-asparaginase has been reviewed by , our effort has been to include recent and updated information about the enzyme covering new aspects such as structural modification and immobilization of L-asparaginase, recombinant L-asparaginase, resistance to L-asparaginase, methods of assay of L-asparagine and L-asparaginase activity using the biosensor approach, L-asparaginase activity in soil and the factors affecting it. Also, side-effects of L-asparaginase treatment in acute lymphoblastic leukemia (ALL) have been discussed in the current review. L-asparaginase has been and is still one of the most widely studied therapeutic enzymes by researchers and scientists worldwide.     

体外法探究猪空肠和回肠黏膜微生物对低聚半乳糖和低聚甘露糖的发酵特性

【背景】小肠黏膜微生物是肠道菌群的重要组成部分,大量研究表明日粮添加低聚半乳糖（galacto-oligosaccharides,GOS）和低聚甘露糖（manno-oligosaccharides,MOS）能够调控猪的大肠菌群结构,但关于其调控小肠黏膜微生物的研究较少。【目的】通过体外发酵法探究猪空肠黏膜和回肠黏膜微生物发酵GOS和MOS的规律。【方法】以生长猪的空肠黏膜微生物和回肠黏膜微生物作为接种物,以GOS和MOS作为底物进行厌氧发酵,在发酵0、6、12、24 h时采样测定总菌数量、pH、氨态氮（ammonia nitrogen,NH₃-N）、菌体蛋白（microbial crude protein,MCP）和有机酸,在24 h收集微生物提取DNA进行细菌定量分析。【结果】在24 h时,回肠黏膜组的NH₃-N浓度显著低于空肠黏膜组,而MCP浓度显著高于空肠黏膜组（P<0.05）。在发酵的前6 h各组pH无明显变化,有机酸积累较少。在12 h时,MOS组的乳酸、乙酸、丁酸和总短链脂肪酸产量显著高于GOS组（P<0.05）,此时只有回肠黏膜组有少量丙酸产生。在24 h时,MOS回肠黏膜组乳酸产量最高而pH值最低（P<0.05）。相较于MOS组,GOS组显著提高了丙酸的产量（P<0.05）。相较于GOS组,MOS组显著提高了乙酸的产量,在空肠黏膜组中显著提高了丁酸和总短链脂肪酸的产量（P<0.05）。定量结果表明,在24 h时,各处理组的厚壁菌门数量都接近总菌数量,属于优势菌门。相较于MOS组,GOS组显著提高了拟杆菌门、链球菌属、韦荣氏球菌属和普拉梭菌细菌的数量,提高了空肠黏膜组中Clostridium cluster IV和回肠黏膜组中Clostridium cluster XIVa的数量（P<0.05）。相较于GOS组,MOS组显著提高了大肠杆菌和乳酸杆菌属的数量,提高了回肠黏膜组中罗氏菌属的数量（P<0.05）。【结论】猪小肠黏膜微生物对GOS和MOS具有不同的发酵模式,主要表现在有机酸的产生和促进细菌的增殖方面。GOS具有产丙酸优势,提高了拟杆菌门和韦荣氏球菌属的数量;MOS促进了乙酸的产生,提高了大肠杆菌和乳酸杆菌的数量。     

电子穿梭体对菌株Clostridium butyricum LQ25异化铁还原性质影响

【目的】在异化铁还原细菌培养体系中,通过外加电子穿梭体,分析电子穿梭体种类与浓度对细菌异化铁还原性质的影响。【方法】以一株发酵型异化铁还原细菌Clostridium butyricum LQ25为研究对象,设置水溶性介体蒽醌-2-磺酸钠和核黄素作为外加电子穿梭体。【结果】在氢氧化铁为电子受体、葡萄糖为电子供体培养条件下,不同浓度蒽醌-2-磺酸钠和核黄素对菌株LQ25异化铁还原效率影响具有显著性差异。外加蒽醌-2-磺酸钠浓度为0.5 mmol/L时,菌株累积产生Fe(Ⅱ)浓度最高,为12.95±0.08 mg/L,相比对照组提高88%。核黄素浓度为100mg/L时,菌株累积产生Fe(Ⅱ)浓度是11.06±0.04mg/L,相比对照组提高61%。外加电子穿梭体能够改变菌株LQ25发酵产物中丁酸和乙酸浓度,提高乙酸相对含量。【结论】蒽醌-2-磺酸钠和核黄素作为外加电子穿梭体能显著促进细菌异化铁还原效率,为揭示发酵型异化铁还原细菌胞外电子传递机制提供实验支持。     

生物竞争排斥对油藏微生物群落结构变化影响

【目的】海上S油田采用生物竞争排斥技术治理油藏硫化氢产出取得一定成效,本研究通过揭示该技术对油藏环境中微生物群落结构的影响,尝试研究硫化氢治理过程中产生效果差异的因素。【方法】采用高通量测序分析等方法对加入硝酸盐、亚硝酸盐等药剂后,治理效果低效井、高效井及未治理井中不同微生物群落结构变化进行分析。【结果】与低效井和未治理井相比,高效井中的反硝化菌和石油降解菌种类和丰度明显增加,其中石油降解菌增加24.14%,反硝化细菌增加5.23%;Fe²⁺、Zn²⁺等离子的存在对不同井间治理效果差异和微生物群落变化具有一定影响。【结论】海上油田硫化氢治理中,生物竞争排斥技术不仅可以明显降低硫化氢产出,同时对油藏微生物群落环境也影响显著,微生物群落结构分析可作为硫化氢治理效果评价的重要指标,为海上油田硫化氢治理工作提供技术支持。     

天然Fe(Ⅱ)矿物-生物质强化微生物还原固定五价钒研究

【目的】重金属钒的环境危害日益受到关注,微生物可实现高毒性的五价钒[pentavalent vanadium, V(Ⅴ)]的还原固定,其中电子供体是微生物还原V(Ⅴ)的关键,尽管天然Fe(Ⅱ)矿物和天然生物质均被报道可单独支持微生物还原V(Ⅴ),而基于两者构建的混养体系中微生物还原V(Ⅴ)的特征尚未揭示。【方法】本研究对天然Fe(Ⅱ)矿物和生物质进行优选并复配组合,探究混养生物体系中五价钒[V(Ⅴ)]的还原机理。【结果】磁黄铁矿和木屑对V(Ⅴ)的去除效率最高,分别为54.2%±3.4%和67.1%±3.1%。当优选的磁黄铁矿与木屑组合复配比例为1:3时可达到最高的V(Ⅴ)去除效率82.7%±3.1%。V(Ⅴ)被还原为不溶性V(Ⅳ)沉淀,Fe(Ⅱ)和S(–Ⅱ)分别被氧化为Fe(Ⅲ)和SO₄^2-。在混养体系中,脱硫菌(Desulfurivibrio)和硫菌属(Thiobacillus)等自养菌属可能参与磁黄铁矿的氧化与V(Ⅴ)还原,并利用无机碳源合成有机中间代谢产物,与无胆甾原体属(Acholeplasma)等纤维素降解菌分解木屑的产物一起,被B...     

Scope and Strategies for Regulation of Nitrification in Agricultural Systems—Challenges and Opportunities

Nitrification, a microbial process, is a key component and integral part of the nitrogen (N) cycle. Soil N is in a constant state of flux, moving and changing chemical forms. During nitrification, a relatively immobile N-form (NH ₄ ⁺) is converted into highly mobile nitrate-N (NO ₃ ^?). The nitrate formed is susceptible to losses via leaching and conversion to gaseous forms via denitrification. Often less than 30% of the applied N fertilizer is recovered in intensive agricultural systems, largely due to losses associated with and following nitrification. Nitrogen-use efficiency (NUE) is defined as the biomass produced per unit of assimilated N and is a conservative function in most biological systems. A better alternative is to define NUE as the dry matter produced per unit N applied and strive for improvements in agronomic yields through N recovery. Suppressing nitrification along with its associated N losses is potentially a key part in any strategy to improve N recovery and agronomic NUE. In many mature N-limited ecosystems, nitrification is reduced to a relatively minor flux. In such systems there is a high degree of internal N cycling with minimal loss of N. In contrast, in most high-production agricultural systems nitrification is a major process in N cycling with the resulting N losses and inefficiencies. This review presents the current state of knowledge on nitrification and associated N losses, and discusses strategies for controlling nitrification in agricultural systems. Limitations of the currently available nitrification inhibitors are highlighted. The concept of biological nitrification inhibition (BNI) is proposed for controlling nitrification in agricultural systems utilizing traits found in natural ecosystems. It is emphasized that suppression of nitrification in agricultural systems is a critical step required for improving agronomic NUE and maintaining environmental quality.     

Protist.guru: A Comparative Transcriptomics Database for Protists

SummaryDuring the last few decades, the study of microbial ecology has been enabled by molecular and genomic data. DNA sequencing has revealed the surprising extent of microbial diversity and how microbial processes run global ecosystems. However, significant gaps in our understanding of the microbial world remain, and one example is that microbial eukaryotes, or protists, are still largely neglected. To address this gap, we used gene expression data from 17 protist species to create protist.guru: an online database equipped with tools for identifying co-expressed genes, gene families, and co-expression clusters enriched for specific biological functions. Here, we show how our database can be used to reveal genes involved in essential pathways, such as the synthesis of secondary carotenoids in Haematococcus lacustris. We expect protist.guru to serve as a valuable resource for protistologists, as well as a catalyst for discoveries and new insights into the biological processes of microbial eukaryotes.AvailabilityThe database and co-expression networks are freely available from http://protist.guru/. The expression matrices and sample annotations are found in the supplementary data.     

Estudio preliminar de la efectividad de la terapia asistida con perros en personas de la tercera edad

IntroductionAnimal-assisted therapy is increasingly present in several educational and health areas. The aim of this study is to assess the effectiveness of such interventions in the elderly population living in residential settings.Materials and methodsA 12-week dog-assisted intervention program was designed, with 16 participants from a nursing home divided into an experimental group and a control group.ResultsSeveral physical and psychological variables were assessed before and after the intervention. While there were no significant differences in the control group, the experimental group improved significantly after participating in the program.DiscussionThe results support the hypothesis that animal-assisted interventions may be beneficial for residents in elderly care homes.     

Production of medium-chain-length PHA in octanoate-fed enrichments dominated by Sphaerotilus sp.

Medium-chain-length polyhydroxyalkanoate (mcl-PHA) production by using microbial enrichments is a promising but largely unexplored approach to obtain elastomeric biomaterials from secondary resources. In this study, several enrichment strategies were tested to select a community with a high mcl-PHA storage capacity when feeding octanoate. On the basis of analysis of the metabolic pathways, the hypothesis was formulated that mcl-PHA production is more favorable under oxygen-limited conditions than short-chain-length PHA (scl-PHA). This hypothesis was confirmed by bioreactor experiments showing that oxygen limitation during the PHA accumulation experiments resulted in a higher fraction of mcl-PHA over scl-PHA (i.e., a PHA content of 76 wt% with an mcl fraction of 0.79 with oxygen limitation, compared to a PHA content of 72 wt% with an mcl-fraction of 0.62 without oxygen limitation). Physicochemical analysis revealed that the extracted PHA could be separated efficiently into a hydroxybutyrate-rich fraction with a higher M_w and a hydroxyhexanoate/hydroxyoctanoate-rich fraction with a lower M_w. The ratio between the two fractions could be adjusted by changing the environmental conditions, such as oxygen availability and pH. Almost all enrichments were dominated by Sphaerotilus sp. This is the first scientific report that links this genus to mcl-PHA production, demonstrating that microbial enrichments can be a powerful tool to explore mcl-PHA biodiversity and to discover novel industrially relevant strains.     

Enhancement of Serum Lysozyme Activity by Injecting a Mixture of Chitosan Oligosaccharides Intravenously in Rabbits

Mycophenolic acid (MPA, 1), an inhibitor of IMP-dehydrogenase (IMPDH) and a latent PPARγ agonist, is used as an effective immunosuppressant for clinical transplantation and recently entered clinical trials in advanced multiple myeloma patients. On the other hand, suberoylanilide hydroxamic acid (SAHA), a non-specific histone deacetylase (HDAC) inhibitor, has been approved for treating cutaneous T-cell lymphoma. MPA seemed to bear a cap, a linker, and a weak metal-binding site as a latent inhibitor of HDAC. Therefore, the hydroxamic acid derivatives of mycophenolic acid having an effective metal-binding site, mycophenolic hydroxamic acid (MPHA, 2), 7-O-acetyl mycophenolic acid (7-O-Ac MPHA, 3), and 7-O-lauroyl mycophenolic hydroxamic acid (7-O-L MPHA, 4) were designed and synthesized. All these compounds inhibited histone deacetylase with IC₅₀ values of 1, 0.9 and 0.5 μM, and cell proliferation at concentrations of 2, 1.5 and 1 μM, respectively.     

The first insight into the trace element status of human adrenal gland accompanied by elemental alterations in adrenal adenomas

BackgroundThe baseline status of trace metals in adrenal tissue is unresolved, while the elemental profile for any adrenal pathology has not been examined so far. This study aimed to determine the baseline status of important toxic (Ni, As, Cd, Pb, Th, U) and essential trace elements (Mn, Co, Cu, Zn, Se) in healthy adrenal tissues (HATs) as well as to examine whether there are alterations in the elemental composition of adenomatous adrenal tissues (AATs). Furthermore, this study aimed to find potential trace metals that could play a role in the pathogenesis of adrenal adenoma (AA).MethodsThe study included 45 patients diagnosed with AA. Impacts of relevant parameters such as gender, age, smoking habits and nodular sizes were considered. All samples were subjected to microwave digestion and the trace elements were determined by inductively coupled plasma mass spectrometry (ICP-MS).ResultsThis is the first study that provided an insight into the elemental status of HATs. It was also shown that AATs had altered trace metal contents. Compared to HATs, the most significant findings were related to the high content of essential (Cu, Mn, Se, Zn) and Pb as a non-essential metal. Although gender, age and smoking habits had a modest effect on metal profiles, the most significant alterations were related to the nodular diameter above 4 cm, indicating that the growth of benign tumor could influence changes in elemental composition.ConclusionFor the first time the baseline contents of essential and toxic trace metals in HATs were determined. The results of this study may highlight the role of toxic and essential trace metals in AAs and could provide new insights into the molecular basis of pathophysiological changes caused by the hazardous effects of trace metals on adrenal structure and function.     

Reduction of Selenium Oxyanions in Wastewater Using Two Bacterial Strains

The biological reduction of selenium oxyanions is capable of reducing both selenate and selenite to insoluble elemental selenium. In this process, however, bacteria inevitably require expensive chemicals such as yeast extract in almost all cases. Therefore, the reduction of selenium oxyanions with inexpensive alcohol would be more practical. A Pseudomonas sp. strain 4C‐C isolated from a sludge in a wastewater treatment facility was able to reduce selenate to selenite using ethanol as an electron donor for its anaerobic respiration, but could not reduce selenite to elemental selenium. Paracoccus denitrificans JCM‐6892, on the other hand, was observed to be able to reduce selenite to elemental selenium in the presence of ethanol, but not selenate to selenite. Therefore, a mixture containing a suspension of Pseudomonas sp. strain 4C‐C and P. denitrificans JCM‐6892 cells allowed selenate to be reduced to insoluble elemental selenium via selenite in the presence of ethanol and was also capable of reducing nitrate to nitrogen gas. Aiming at simplicity of the recovery process of insoluble elemental selenium, a polymeric gel immobilized mixture of the two bacterial strains was examined using ethanol as an electron donor. The immobilized mixture could therefore reduce not only selenate to elemental selenium, but also nitrate to nitrogen gas in a single step. The gel that immobilized the microbial mixture changed its color during the process to bright red and no red elemental selenium was left in the wastewater. This indicates that the reduced elemental selenium was completely absorbed in the gel. This simple bacterial combination would therefore be effective in the presence of ethanol to reduce selenium oxyanions in various wastewaters containing selenium and the other oxyanions.     

Origin of microbial life: Nano- and molecular events, thermodynamics/entropy, quantum mechanisms and genetic instructions

Currently, there are no agreed upon mechanisms and supporting evidence for the origin of the first microbial cells on the Earth. However, some hypotheses have been proposed with minimal supporting evidence and experimentation/observations. The approach taken in this article is that life originated at the nano- and molecular levels of biological organization, using quantum mechanic principles that became manifested as classical microbial cell(s), allowing the origin of microbial life on the Earth with a core or minimal, organic, genetic code containing the correct instructions for cell(s) for growth and division, in a micron dimension environment, with a local entropy range conducive to life (present about 4 billion years ago), and obeying the laws of thermodynamics. An integrated approach that explores all encompassing factors necessary for the origin of life, may bring forth plausible hypotheses (and mechanisms) with much needed supporting experimentation and observations for an origin of life theory.     

The sweet spot for biologics: recent advances in characterization of biotherapeutic glycoproteins

Introduction: Glycosylation is recognized as a Critical Quality Attribute for therapeutic glycoproteins such as monoclonal antibodies, fusion proteins and therapeutic replacement enzymes. Hence, efficient and quantitative glycan analysis techniques have been increasingly important for their discovery, development and quality control. The aim of this review is to highlight relevant and recent advances in analytical technologies for characterization of biotherapeutic glycoproteins.

Areas covered: The review gives an overview of the glycosylation trends of biotherapeutics approved in 2016 and 2017 by FDA. It describes current and novel analytical technologies for characterization of therapeutic glycoproteins and is explored in the context of released glycan, glycopeptide or intact glycoprotein analysis. Ultra performance liquid chromatography, mass spectrometry and capillary electrophoresis technologies are explored in this context.

Expert commentary: There is a need for the biopharmaceutical industry to incorporate novel state of the art analytical technologies into existing and new therapeutic glycoprotein workflows for safer and more efficient biotherapeutics and for the improvement of future biotherapeutic design. Additionally, at present, there is no ‘gold-standard’ approach to address all the regulatory requirements and as such this will involve the use of orthogonal glycoanalytical technologies with a view to gain diagnostic information about the therapeutic glycoprotein.     

Explore mediated co-varying dynamics in microbial community using integrated local similarity and liquid association analysis

Background

Discovering the key microbial species and environmental factors of microbial community and characterizing their relationships with other members are critical to ecosystem studies. The microbial co-occurrence patterns across a variety of environmental settings have been extensively characterized. However, previous studies were limited by their restriction toward pairwise relationships, while there was ample evidence of third-party mediated co-occurrence in microbial communities.

Methods

We implemented and applied the triplet-based liquid association analysis in combination with the local similarity analysis procedure to microbial ecology data. We developed an intuitive scheme to visualize those complex triplet associations along with pairwise correlations. Using a time series from the marine microbial ecosystem as example, we identified pairs of operational taxonomic units (OTUs) where the strength of their associations appeared to relate to the values of a third “mediator” variable. These “mediator” variables appear to modulate the associations between pairs of bacteria.

Results

Using this analysis, we were able to assess the OTUs’ ability to regulate its functional partners in the community, typically not manifested in the pairwise correlation patterns. For example, we identified Flavobacteria as a multifaceted player in the marine microbial ecosystem, and its clades were involved in mediating other OTU pairs. By contrast, SAR11 clades were not active mediators of the community, despite being abundant and highly correlated with other OTUs. Our results suggested that Flavobacteria are more likely to respond to situations where particles and unusual sources of dissolved organic material are prevalent, such as after a plankton bloom. On the other hand, SAR11s are oligotrophic chemoheterotrophs with inflexible metabolisms, and their relationships with other organisms may be less governed by environmental or biological factors.

Conclusions

By integrating liquid association with local similarity analysis to explore the mediated co-varying dynamics, we presented a novel perspective and a useful toolkit to analyze and interpret time series data from microbial community. Our augmented association network analysis is thus more representative of the true underlying dynamic structure of the microbial community. The analytic software in this study was implemented as new functionalities of the ELSA (Extended local similarity analysis) tool, which is available for free download (http://bitbucket.org/charade/elsa).