The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide

One of the major factors associated with global change is the ever-increasing concentration of atmospheric CO₂. Although the stimulating effects of elevated CO₂ (eCO₂) on plant growth and primary productivity have been established, its impacts on the diversity and function of soil microbial communities are poorly understood. In this study, phylogenetic microarrays (PhyloChip) were used to comprehensively survey the richness, composition and structure of soil microbial communities in a grassland experiment subjected to two CO₂ conditions (ambient, 368 p.p.m., versus elevated, 560 p.p.m.) for 10 years. The richness based on the detected number of operational taxonomic units (OTUs) significantly decreased under eCO₂. PhyloChip detected 2269 OTUs derived from 45 phyla (including two from Archaea), 55 classes, 99 orders, 164 families and 190 subfamilies. Also, the signal intensity of five phyla (Crenarchaeota, Chloroflexi, OP10, OP9/JS1, Verrucomicrobia) significantly decreased at eCO₂, and such significant effects of eCO₂ on microbial composition were also observed at the class or lower taxonomic levels for most abundant phyla, such as Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria, suggesting a shift in microbial community composition at eCO₂. Additionally, statistical analyses showed that the overall taxonomic structure of soil microbial communities was altered at eCO₂. Mantel tests indicated that such changes in species richness, composition and structure of soil microbial communities were closely correlated with soil and plant properties. This study provides insights into our understanding of shifts in the richness, composition and structure of soil microbial communities under eCO₂ and environmental factors shaping the microbial community structure.     

Considering external information to improve the phylogenetic comparison of microbial communities: a new approach based on constrained Double Principal Coordinates Analysis (cDPCoA)

The use of next‐generation sequencing technologies is revolutionizing microbial ecology by allowing a deep phylogenetic coverage of tens to thousands of samples simultaneously. Double Principal Coordinates Analysis (DPCoA) is a multivariate method, developed in community ecology, able to integrate a distance matrix describing differences among species (e.g. phylogenetic distances) in the analysis of a species abundance matrix. This ordination technique has been used recently to describe microbial communities taking into account phylogenetic relatedness. In this work, we extend DPCoA to integrate the information of external variables measured on communities. The constrained Double Principal Coordinates Analysis (cDPCoA) is able to enforce a priori classifications to retrieve subtle differences and (or) remove the effect of confounding factors. We describe the main principles of this new approach and demonstrate its usefulness by providing application examples based on published 16S rRNA gene data sets.     

Recent advances in molecular techniques for the detection of phylogenetic markers and functional genes in microbial communities

The detection and analysis of nucleic acids extracted from microbial communities are the ultimate ways to determine the diversity and functional capability of microbial communities in the environments. However, it remains a challenge to use molecular techniques for unequivocal determination and quantification of microbial species composition and functional activities. Considerable efforts have been made to enhance the capability of molecular techniques. Here an update of the recent developments in molecular techniques for environmental microbiology is provided.     

系统生物技术在工业(药用)微生物菌种选育与高通量筛选中的应用

系统生物学时代,各种高通量组学技术产生了大量数据。一些旨在挖掘数据和整合信息的计算机建模技术也逐渐用于系统水平定量分析细胞代谢。模型有助于指导实验设计,实验结果反过来检验和优化模型,虚实结合,有利于在系统层面认识复杂的代谢过程。根据这些信息,可以设计、优化工业微生物代谢特征,高表达目标代谢物。本文综述了系统生物技术在工业(药用)微生物育种和高通量筛选中的最新应用进展。     

Designing synthetic microbial communities for effectual bioremediation: A review

Abstract

Bioremediation is a better alternative and widely accepted approach used for efficient degradation of environmental pollutants released from industries, urban and agricultural activities due to its eco-friendly nature. Systems biology helps in the identification of new genes, proteins, metabolites, and metabolic pathways involved in bioremediation. Such information can be used for designing synthetic microbial communities that can degrade multiple recalcitrant pollutants simultaneously. This review gives a brief insight into various systems biology tools towards providing a greater understanding of microbial behaviour and improving the way of bioremediation. These techniques alone or in combination, provide a way to understand and improve the genetic potential of microorganisms to remediate various environmental contaminants efficiently. Further, this review also describes the successful employment of synthetic microbial consortium in the bioremediation. Moreover, In-silico tools are also described to analyse the data obtained through different laboratory experiments as well to predict the behaviour of microbial consortium towards the pollutants using different databases.     

应用多重PCR鉴定微生物肥料常用芽孢杆菌

[目的]枯草群芽孢杆菌中枯草芽孢杆菌(Bacillus subtilis)、解淀粉芽孢杆菌(B.amyloliq-wefaciens)、地衣芽孢杆菌(B.licheniformis)和短小芽孢杆菌(B.pumilus)是微生物肥料中常用菌种,用传统方法鉴定费时费力,有必要建立检测和鉴定这些芽孢杆菌的种特异性PCR方法.[方法]利用已登录的gyrA、rpoA和16s rRNA基因序列分别设计和筛选上述菌种的特异引物并建立多重PCR反应体系.[结果]以基因组DNA为模板,扩增芽孢杆菌、类芽孢杆菌和短芽孢杆菌3属15种的标准菌株(共33株),4个目标种分别产生了大小不同的唯一的产物,除个别种与短小芽孢杆菌引物有交叉反应外,其余参考菌株均为阴性.从23株枯草群菌株的基因组DNA扩增发现,PCR鉴定与常规鉴定结果一致.[结论]本文建立的多重PCR方法具有较好的特异性,可快速准确鉴定枯草群的4个种,在微生物肥料检测方面有良好的实用前景.     

A phylogenetic approach to the identification of phosphoglucomutase genes

The expanding molecular database provides unparalleled opportunities for characterizing genes and for studying groups of related genes. We use sequences drawn from the database to construct an evolutionary framework for examining the important glycolytic enzyme phosphoglucomutase (PGM). Phosphoglucomutase plays a pivotal role in the synthesis and utilization of glycogen and is present in all organisms. In humans, there are three well-described isozymes, PGMI, PGM2, and PGM3. PGM1 was cloned 5 years ago; however, repeated attempts using both immunological approaches and molecular probes designed from PGM1 have failed to isolate either PGM2 or PGM3. Using a phylogenetic strategy, we first identified 47 highly divergent prokaryotic and eukaryotic PGM-like sequences from the database. Although overall amino acid identity often fell below 20%, the relative order, position, and sequence of three structural motifs, the active site and the magnesium-- and sugar-binding sites, were conserved in all 47 sequences. The phylogenetic history of these sequences was complex and marked by duplications and translocations; two instances of transkingdom horizontal gene transfer were identified. Nonetheless, the sequences fell within six well-defined evolutionary lineages, three of which contained only prokaryotes. Of the two prokaryotic/eukaryotic lineages, one contained bacterial, yeast, slimemold, invertebrate, and vertebrate homologs to human PGM1 and the second contained likely homologs to human PGM2. Indeed, an amino acid sequence, derived from a partial human cDNA, that fell within the second cross-kingdom lineage bears several characteristics expected for PGM2. A third lineage may contain homologs to human PGM3. On a general level, our phylogenetic-based approach shows promise for the further utilization of the extensive molecular database.      

A phylogenetic approach to the evolution of fish behaviour

Summary WHAT HAVE WE LEARNED?As I indicated in the introduction, this is a non-traditional review. I have not asked What generalizations can we draw about the evolution of fish behaviour based upon information gleaned from phylogenetically based studies? Instead, I have presented detailed discussions of those studies. The reason for this approach is quite simple: if all studies in such a wide area of investigation can be discussed at length in one relatively short paper, then the database is not large enough to warrant the move from information collection to information synthesis. The purpose of this review, then, has been to capture the enthusiasm of the phylogenetically orientated fish ethologists and to highlight their discoveries, in the hopes that this will stimulate further research. If successful, the next review of phylogeny and the evolution of fish behaviour will follow a more familiar pathway.Although the database does not allow us to draw generalizations about the evolution of specific behavioural characters in fishes, the studies to date have uncovered a number of more general evolutionary insights. First, phylogenetic conservatism is evident at all levels of analysis, from the muscle activity patterns that underlie behavioural characters (Lauder 1986; Westneat and Wainwright, 1989; Westneat 1991; Wainwright and Lauder, 1992) through foraging preferences (Winterbottom and McLennan, 1993) and egg deposition strategies (Johnston and Page, 1992) to parental care (Stiassney and Gerstner, 1992). This conservatism forms the backbone against which the appearance of novel behaviours (apomorphies) can be highlighted. Each species' behavioural repertoire is thus a unique combination of very old (plesiomorphic), relatively old (synapomorphic) and recently derived (autapomorphic) characters. Second, phylogenetic analysis has allowed us to investigate models of behavioural evolution that were constructed from a variety of microevolutionary fitness parameters. The macroevolutionary patterns have corroborated some parts of those models (transition from biparental to female-only care: Gross and Sargent, 1985; Stiassney and Gerstner, 1992; transition from fresh water to anadromy: Gross et al., 1988; Stearley, 1992) and highlighted other parts of the models that would benefit from a re-examination of the basic assumptions (transition from biparental or female-only to male-only care: Gross and Sargent, 1985; Stiassney and Gerstner, 1992). Third, expanding our evolutionary perspective to include clades of organisms has allowed researchers to formulate new theories of behavioural evolution incroporating information about the patterns of character origin and diversification as well as information about character maintenance (Ryan, 1900a; Ryan and Rand, 1990; Ryan et al., 1990a). And finally, examination of macroevolutionary correlations between the origin and diversification of behavioural characters has allowed us to make predictions about the forces influencing the evolution of those characters that can then be tested experimentally (McLennan et al., 1988; Basolo, 1990a,b, 1991; McLennan, 1991). The studies presented in this paper have spanned a wide theoretical arena. They have revealed a number of interesting insights about the evolution of behaviour, and in so doing, have demonstrated the hybrid vigour of a research programme based upon integrating phylogeny and experimental ethology, phylogeny and functional morphology, and phylogeny and behavioural ecology. The question to be answered now is:WHERE DO WE GO FROM HERE?If this fledgling research programme is to remain vigorous, we need to do two things. First, channels of communication must be re-opened between systematists and ethologists. Specifically, we need to encourage systematists to construct robust phylogenetic trees for groups of fish that either have already been well studied behaviourally and ecologically, or would be of interest to ethologists if a phylogeny existed (the belontiids, poeciliids, and rivulines come to mind, to name just a few). In the absence of such critical information, behavioural ecologists are faced with the option of investigating their ethological data based upon trees reconstructed from old classification schemes or phenograms, neither of which produces a robust phylogenetic hypothesis of genealogy. Researchers who have opted for this approach preface their investigations with the caveat that the analysis and conclusions are only preliminary because of the unsatisfactory nature of the phylogenetic hypotheses available to them. The importance of a preliminary analysis cannot be understimated for researchers who are frustrated by their inability to apply the phylogenetic approach to their burgeoning data sets. It is, however, critical to remember that a preliminary analysis can, at best, produce only tentative results. If the data themselves are both incomplete and ambiguous, this will compound the problems arising from the absence of a rigorous phylogenetic framework, which will produce a confusing picture of behavioural evolution. It is also important to realize that even the most robust phylogenetic tree is still only a hypothesis of genealogical relationships, a hypothesis that may change with the discovery of new data.Second, links must be forged between comparative ethology and behavioural ecology. All of the examples discussed in this paper uncovered a phylogenetic component in patterns of behavioural origin and diversification. The discovery of this phylogenetic influence, however, is only the first step in developing a comprehensive evolutionary picture because phylogenetic patterns can tell us very little about the processes underlying those patterns. In order to explore questions of process, we must incorporate information about the fitness parameters of behavioural characters into our evolutionary picture. For example, optimizing such parameters onto a phylogenetic tree may allow us to investigate whether there are any macroevolutionary correlations between the origin and divergence of a behaviour and a change in one (or more) of the fitness components. We must also incorporate information about the genetic, developmental and physiological control of behaviour into our comparative framework (Brooks and McLennan, 1991; Willis et al., 1991; Lauder et al., 1993). This is perhaps the most neglected aspect of comparative ethology and will thus be the most difficult to remedy. Details of the genetic and developmental systems underlying behaviour are known for only a handful of taxa and for only a handful of behaviours within those taxa. The physiological control of behaviour is better studied, but has yet to be placed within a phylogenetic context (but see e.g. Stearley, 1992, for an example of the insights that can be gained from such a study). The results of such a multilevel approach will be a more robust estimate of the relative roles for the effects of both phylogenetic heritage and environmental factors in the evolution of behaviour in fishes.     

An overview on biodegradation of polystyrene and modified polystyrene: the microbial approach

Polystyrene is a widely used plastic in many aspects of human life and in industries due to its useful characteristics of low cost, light weight, ease of manufacture, versatility, thermal efficiency, durability, and moisture resistance. However, polystyrene is very stable and extremely hard to degrade in the environment after disposal. Polystyrene can be used as a carbon source for microorganisms similar to many other hydrocarbons. The ability of microorganisms to use polystyrene as a carbon source has been recently established. However, the high molecular weight of polystyrene limits its use as a substrate for enzymatic reactions to take place. In this paper, we review studies on biodegradation of polystyrene to give an overview and direction for future studies.     

A chemocentric approach to the identification of cancer targets

A novel chemocentric approach to identifying cancer-relevant targets is introduced. Starting with a large chemical collection, the strategy uses the list of small molecule hits arising from a differential cytotoxicity screening on tumor HCT116 and normal MRC-5 cell lines to identify proteins associated with cancer emerging from a differential virtual target profiling of the most selective compounds detected in both cell lines. It is shown that this smart combination of differential in vitro and in silico screenings (DIVISS) is capable of detecting a list of proteins that are already well accepted cancer drug targets, while complementing it with additional proteins that, targeted selectively or in combination with others, could lead to synergistic benefits for cancer therapeutics. The complete list of 115 proteins identified as being hit uniquely by compounds showing selective antiproliferative effects for tumor cell lines is provided.     

Anti-CRISPR Discovery: Using Magnets to Find Needles in Haystacks

CRISPR-Cas immune systems in bacteria and archaea protect against viral infection, which has spurred viruses to develop dedicated inhibitors of these systems called anti-CRISPRs (Acrs). Like most host-virus arms races, many diverse examples of these immune and counter-immune proteins are encoded by the genomes of bacteria, archaea, and their viruses. For the case of Acrs, it is almost certain that just a small minority of nature’s true diversity has been described. In this review, I discuss the various approaches used to identify these Acrs and speculate on the future for Acr discovery. Because Acrs can determine infection outcomes in nature and regulate CRISPR-Cas activities in applied settings, they have a dual importance to both host-virus conflicts and emerging biotechnologies. Thus, revealing the largely hidden world of Acrs should provide important lessons in microbiology that have the potential to ripple far beyond the field.     

Comparative phylogenetic analysis of microbial communities in pristine and hydrocarbon-contaminated Alpine soils

A molecular characterization of pristine and petroleum hydrocarbon-contaminated Alpine soils sampled in Tyrol (Austria) was performed. To identify predominant bacteria, PCR-amplified 16S rRNA gene fragments from five pristine and nine contaminated soils were analysed using denaturing gradient gel electrophoresis (DGGE). Sequencing and phylogenetic analyses demonstrated that the majority of the DGGE bands represented bacteria in the Actinobacteria and Proteobacteria phyla: 18 and 73%, respectively, in pristine soils, compared with 20 and 76%, respectively, in contaminated soils. A different distribution pattern of bacterial classes in the Proteobacteria was observed between pristine and contaminated soils. The relative proportion of microorganisms belonging to the Alphaproteobacteria was larger in pristine (46%) than in contaminated (24%) soils, while Betaproteobacteria and Gammaproteobacteria were detected only in the hydrocarbon-contaminated soils. This result compared favourably with earlier work in which hydrocarbon-degradation genotypes, largely pseudomonads and Acinetobacter, belonging to the Gammaproteobacteria, were enriched following oil hydrocarbon contamination. In contrast, members of the Actinobacteria phylum, represented by Rhodococcus and Mycobacterium, were found in pristine soils where contamination events had not occurred. The results demonstrate a significant shift in the microbial community structure in Alpine soils following contamination. Furthermore, more potentially novel phylotypes were found in the pristine soils than in the contaminated soils.     

A graph theoretic approach to the development of minimal phylogenetic trees

Summary The problem of determining the minimal phylogenetic tree is discussed in relation to graph theory. It is shown that this problem is an example of the Steiner problem in graphs which is to connect a set of points by a minimal length network where new points can be added. There is no reported method of solving realistically-sized Steiner problems in reasonable computing time. A heuristic method of approaching the phylogenetic problem is presented, together with a worked example with 7 mammalian cytochrome c sequences. It is shown in this case that the method develops a phylogenetic tree that has the smallest possible number of amino acid replacements. The potential and limitations of the method are discussed. It is stressed that objective methods must be used for comparing different trees. In particular it should be determined how close a given tree is to a mathematically determined lower bound. A theorem is proved which is used to establish a lower bound on the length of any tree and if a tree is found with a length equal to the lower bound, then no shorter tree can exist.     

A molecular biological approach to the phylogenetic position of the genus Hyperamoeba

In 1923 Alexeieff described a new amoebic species within a new genus and named it Hyperamoeba flagellata. This amoeba exhibits three life cycle stages, an amoeboid trophozoite, a flagellated stage, and a cyst-like the heteroloboseans, the mastigamoebae, and several slime moulds. Since then more strains have been isolated and relationships to the protostelids and cercomonads and to the myxogastrid plasmodial slime moulds have been suggested. However, up to now the classification and phylogenetic position of the hyperamoebae has remained unclear. The aim of our study was to make an approach to the phylogeny of the genus Hyperamoeba with combined morphological and molecular biological data. Since 1988 we have isolated and collected Hyperamoeba-like strains from different aquatic and terrestrial sources. The 18S rDNA-sequences of 8 new Hyperamoeba strains isolated from various habitats were analysed and a cluster analysis was performed including all other available hyperamoebae. Altogether, the results of our study corroborate the relatedness of Hyperamoeba to various slime moulds. However, the hyperamoebae do not seem to be a monophyletic group, clearly putting the validity of the genus Hyperamoeba into question.     

荒漠草地土壤微生物生物量和微生物熵对沙漠化的响应

采用空间序列代替时间演替的方法,分析宁夏中北部盐池县荒漠草地不同沙漠化阶段(荒漠草地、固定沙地、半固定沙地和流动沙地)土壤微生物生物量(SMB)和微生物熵(qMB)的变化特征及其影响因子.结果表明:从荒漠草地到流动沙地,土壤微生物生物量碳、氮、磷分别降低46.1%、80.8%和30.0%.随着荒漠草地沙漠化程度的加剧,土壤微生物熵碳(qMBC)、土壤微生物熵氮(qMBN)、土壤微生物熵磷(qMBP)均表现为荒漠草地>固定沙地>半固定沙地>流动沙地,而土壤-微生物化学计量不平衡性(C∶Nimb、C∶Pimb、N∶Pimb)基本呈增加趋势.土壤微生物生物量氮与C∶Nimb呈显著正相关,与N∶Pimb呈显著负相关;土壤微生物生物量磷与C∶Pimb呈显著正相关.冗余分析(RDA)显示,土壤生态化学计量(C∶N、C∶P)对微生物熵碳的负效应最明显.荒漠草地沙漠化显著影响土壤微生物生物量和微生物熵.     

Novel approach using substrate-mediated radiolabelling of RNA to link metabolic function with the structure of microbial communities

A novel concept was developed applying radioisotope-labelled substrate incorporation into the biomass. The resulting radiolabelled RNA was used both as an indicator of activity and as a template for gaining structural and functional information about a substrate-utilizing microbial community. Sequences of PCR products are separated via cloning or using molecular fingerprinting techniques. Nucleic acids from predominant clones or the whole molecular fingerprinting pattern are transferred to a membrane and hybridized with the radiolabelled sample RNA. Scanning of the hybridized blots for radioactivity indicates the members involved in the utilization of the substrate. This novel 'random walk' approach using radioisotope probing was evaluated in a model community experiment.     

土壤微生物总活性研究方法进展

微生物总活性是指在某一时段内微生物所有生命活动的总和,它直接决定着微生物行使生理、生态功能的能力,是微生物学研究的热点,也是难点。迄今为止,还没有建立直接测定微生物总活性的方法,只能用一些相关指标来间接反映它。目前常用的指标主要包括微生物的呼吸速率、生长速率以及胞内RNA含量等。与其它一些基质和环境相比,测定土壤中的微生物总活性更为困难。通过总结研究土壤微生物总活性常用的3种方法,在简略概括传统的土壤微生物呼吸测定法的基础上,详细介绍了放射性同位素标记法和RNA直接表征法的原理和操作流程,整理归纳了一些重要应用案例,比较分析了不同方法的优缺点,以期为选择研究土壤微生物总活性的适宜方法提供依据。     

A thermodynamic theory of microbial growth

Our ability to model the growth of microbes only relies on empirical laws, fundamentally restricting our understanding and predictive capacity in many environmental systems. In particular, the link between energy balances and growth dynamics is still not understood. Here we demonstrate a microbial growth equation relying on an explicit theoretical ground sustained by Boltzmann statistics, thus establishing a relationship between microbial growth rate and available energy. The validity of our equation was then questioned by analyzing the microbial isotopic fractionation phenomenon, which can be viewed as a kinetic consequence of the differences in energy contents of isotopic isomers used for growth. We illustrate how the associated theoretical predictions are actually consistent with recent experimental evidences. Our work links microbial population dynamics to the thermodynamic driving forces of the ecosystem, which opens the door to many biotechnological and ecological developments.