Research Progress of Microbial Diversity in Recent Three Years

ZHAO Meng-meng, XUE Lin-gui

(Schl. of Chem. & Bio-Engin., Key Lab. of Extreme Environ. Microb. Res. & Engin., Lanzhou Jiaotong Uni., Lanzhou 730070)



Research Progress of Microbial Diversity in Recent Three Years

ZHAO Meng-meng, XUE Lin-gui

(Schl.ofChem. &Bio-Engin.,KeyLab.ofExtremeEnviron.Microb.Res. &Engin.,LanzhouJiaotongUni.,Lanzhou730070)

The general situation and latest research trends in the research field of microbial diversity were summarized in this article, including the number of articles in different years, in different databases, in and different research objects which the researchers prefer to select. The papers are categorized into different research emphasis and detailed the corresponding research content in recent 3 years. This review provides us insights into the broader framework of microbial diversity in recent years and represents the research emphasis in this field. The purpose of this article is to provide a research basis for scholars to choose research direction and determine their research content.

research progress; microbial diversity; recent three years

Microbes are everywhere, in soil, water, air or some artificial equipment. Does the existence of microbes have important influence on the structure and function of the ecological environment? Are there interactive relationships between microbes? To find answers to these questions, researchers have made great efforts on these areas. Microbial diversity is the study about microbial ecology; it focuses on the relationship between microbes, microbes and other organisms, microbes and environments. From many years ago, the scholars have done great deal of work in these areas.

As early as 1980, there were few studies concentrated on the research of microbial diversity, because little about the species of microbes was known, so the focus of the work was clustered on the discovery of new species in different environments. It was found that the microbial community diversity was analyzed around 1980, they identified three types of spirilla, two types ofSpirochaetasp., two types ofDesulfovibriasp., a new strain of redBeneckeaand four distinctive unidentified coccoid and filamentous bacteria in Laguna Figueroa, Baja California and Mexico[1]. Then the symbiotic microbial community of the sonoran desert termite was considered by Leleng et al.[2], they were estimated more than 40 interaction species contained in the symbiotic system. The researchers also concerned with the species of hydrocarbon degrading bacteria, lignin degrading bacteria were discussed[3].Around 1990s, the number of related articles increased and most of the scholars were willing to put "microbial diversity" into the title of their articles. Using Elsevier database as an example, from 1975 to 1985, the number of relevant articles were about 29, between 1985 and 1995, 104 articles were found (Fig.1). This showed that more and more scientists devote into the research fields. In this period, the research direction became more diverse, the study object became clearer. Especially the environment where the research object existed was more complex. They discussed the microbial density, composition and diversity in corky root of tomatoes[4], studied the bacterial abundance, bacterial biomass in the upper column of the black sea[5], investigated the microbial abundance and activity from three coal ash basins[6]. By twenty-first century, the number of relevant articles was 10 times than before, the papers tend to be more diversified in methods and experimental design, the breadth and depth of the paper were deepening, the purpose of the study is to find out the interactive relationship between the microbes, microbes and animals or plants, microbes and the environments, in order to clarified the response between the environments and the microbes. They indicated how the tree-based intercropping systems influenced the diversity and stability of soil microbial communities[7]; studied when the 14 years of conversion of grassland to organic agriculture, the response in soil physico-chemical properties and microbial functional diversity[8]. The research area not only rested on the nature environments but also expanded to the field of Engineering, various of bioreactor became the main research object[9-10]. Now, the first ten years of twenty-first century have elapsed, the research about microbial diversity has been a great development both in quality and quantity. This paper summarized the related articles in recent 3 years, providing reference to the other researchers.

Fig.1 The number of articles related to microbial diversity in three databases during 1975-2014

1 Research overview in recent 3 years

To understand the general trend in the research field of microbial diversity from 2012 to 2015, the following chart will give some information (Fig.2, Fig.3, and Fig.4).

Fig.2 The number of papers retrieved in all fields and in title, key words and abstract of three databases

Fig.3 The number of papers retrieved in all fields and in title, key words and abstract of Elsevier database

Fig.4 The number of papers search across from Elsevier database through different keywords

From the charts above, in the database of Chinese Academy of Sciences, it was found the number of the papers related to the field of microbial diversity in Elsevier database were the most. In addition, it was also researched the other big databases, like Springer, Wiley, ACS and PNAS databases, of course, Nature and Science, the world’s top journal database were also in the search range. The information acquired has the same tendency (because of the number of the papers related to the research field in Nature, Science, ACS and PNAS are relatively little, so the first three databases were used as an example to creating charts). The results indicated, during 2012-2015, the total number of articles related to microbial diversity attained to 52 789 in three big databases, the number of papers which the key words contained in the title, abstract were reached 1 740(Fig.2). Specifically, The data in Nature database showed that there are about 555 papers (the key words were contained in all fields), 17 papers (the key words were contained in title, key words and abstract), about 257 papers (the key words were contained in all fields), 18 papers (the key words were contained in title, key words and abstract) in Science database. Different environment has different microbial diversity, different microbial diversity symbolized different meaning, and it represented different functions, structures and the relationship between microbes and environments or other organisms. Taking the Elsevier database as an example, using the microbial diversity and water, microbial diversity and soil, microbial diversity and sludge, microbial diversity and bioreactor as key words respectively, the results retrieved from the database revealed that the papers in the field of water were the most, in the field of soil were second, sludge and bioreactor were less (Fig.3). To have a better understanding on the effect of microbial diversity on environments, the interactive study between different environments is inevitable. Different key words were used for cross searching in the field of title, keywords and abstract, including microbial diversity and water and soil (MD&WSo), microbial diversity and water and bioreactor (MD&WB), microbial diversity and soil and bioreactor (MD&SoB), microbial diversity and water and sludge (MD&WSI), microbial diversity and soil and sludge (MD&SoSI), microbial diversity and bioreactor and sludge (MD&BSI). It was found that the number of the research in the fields of water and soil is the most, in the fields of bioreactor and sludge is also more (Fig.4). Through the data retrieved from the database, it could understand that the general situation in this research field.

2 Research progress in the past 3 years

With the further study and research on microbial diversity, the SCI papers have the obvious tendency. The research area become more diversified, the research method become more changeable, the research object is clearer and the research result is more meaningful. From about 1 500 articles (which the key words were contained in the title, abstract and key words) checked in SCI databases, the contents and divided them into different research groups was summarized.

2.1 Only focus on microbial diversity and discover new species

There were most of articles which studied the microbial diversity in different environments under different conditions. They only described the conditions in that specific environment, identified new species and afforded the research basis to the follow-up study. Catherine et al.[11]investigated the microbial diversity, stability and resilience of the human gut microbiota. Nie et al.[12]considered the microbial diversity in traditional fermentation of Shanxi aged vinegar and discussed the quantities of fungal and bacterial in the different stages of the fermentation. Davide et al.[13]researched the microbial diversity and dynamicity of biogas reactors and compared the microbial dynamicity in response to change of feedstock composition of biogas reactors. Wagener et al.[14]discussed the diversity of intrauterine microbial communities in postpartum dairy cows. Varsik et al.[15]studied the microbial diversity in phyllosphere and laimosphere of different desert plants. Berlendis et al.[16]researched the microbial diversity of the Autun black shale and Graissessac coal. Elizabeth et al.[17]discussed the microbial diversity in the raw goat milk on the different stages of lactation. Vibeke et al.[18]studied the microbial diversity in sinus infections of cystic fibrosis patients and the result showed a higher abundance of classic CF pathogens e.g.PseudomonasaeruginosaandStaphylococcusaureuscompared with the anaerobePropionibacteriumacnes. Silva et al.[19]analyzed the diversity of microbial community in petroleum samples from Brazilian oil fields. Fernand et al.[20]studied the microbial diversity of domestic wastewater in the full-scale sequencing batch reactor (SBR) in Brazil. Bharath et al.[21]analyzed the microbial diversity in the process of triethylamine (TEA) removed by gas phase bio-filter from air. Ajay et al.[22]studied the microbial diversity in an organic vegetable production system covered crops and composted. Specifically,Naturereported on April 2014[23], in North east India, there is a biodiversity hotspot. Scholars worked in North-Eastern Hill University in Shillong developed a web-based microbe database that details information about soil microbes in north east India, this database was established on the analysis of microbial diversity.

2.2 Study on microbial functional diversity

Some studies focused on the function diversity of microbial by analyzing the species diversity of microbial. They investigated the composition of microbial to explain the influence of the microbial on the research systems. On June,Nature[24]had accepted a Japanese invitation; the articles discussed the function and diversity of the healthy human microbiome and delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome. Similarly, in the journal ofScience, Fierer et al.[25]reconstructed the soil microbial diversity and function that once existed in this biome by analyzing relict prairie soils and found that the biogeographical patterns were largely driven by changes in the relative abundance of Verrucomicrobia, a poorly studied bacterial phylum that appears to dominate many prairie soils. Yu et al.[26]studied the microbial function diversity in the rhizospheric surrounding mulberry subjected to long-term fertilization. The results suggested that fertilization had a statistically significant impact on the soil microbial functional diversity. The soil microbial functional diversity generally increased when organic and inorganic fertilizers were applied. Long-term urea and no fertilizer application caused significant microbial functional diversity decline. The analysis indicated that most microbial parameters were mainly correlated with the soil organic matter content. Li et al.[27]studied the changes in soil microbial function diversity with a nitrogen gradient in soil columns. The findings indicated that changes in soil microbial functional diversity can occur with a nitrogen gradient. The extent of changes depends on the nitrogen concentration and the form of inorganic fertilizer. Benjamin et al.[28]considered the microbial function diversity in early recovery of advanced mine. The study has shown that soil microbial is a valuable tool to assess restoration progress, and that ecosystem restoration can begin in a relatively short time following investment in appropriate restoration strategy. Zhang et al.[29]discussed the changes in soil microbial functional diversity under different vegetation restoration patterns for Hulunbeier Sandy Land. They found the vegetation restoration enhanced the functional diversity of microbial community in sandy soil. Andersen et al.[30]discussed the microbial functional diversity in a restored bog approach natural conditions 10 years post restoration. They discovered the microbial functional diversity was shifted towards values observed under natural and unrestored vegetated conditions. Yinghua Xu et al.[31]determined the effects of a wildfire on soil microbial functional diversity in short-term time scales. The result demonstrated the soil microbial community structure in the burned area changed dynamically in monthly scale time following the fire. Microbial species evenness of the burned soil may recover the pre-fire level 1 year after the fire and some microorganism are more sensitive to fire than other species.

2.3 Research on the effect of the changes in microbial diversity on other microbial species or plants and vice versa

If the research on the microbial diversity in a circumstance is the basic work, then research on the influence among different kinds of microorganism is the further work. Discussed the changes of microbial diversity could further elucidated its function in the micro-ecology.

Didienne et al.[32]discussed the relationship between microbial biofilm on wooden vats (‘gerles’) in PDO salers cheese and the pathogen in the milk. They indicated the microbial biofilms from ‘gerles’ play an important role in preventing pathogen development. Bonanomi et al.[33]have given the answer to whether the fungal diversity affects soil fungistasis and bacterial invasion and they concluded that loss of fungal microbial diversity may adversely affect ecosystem functionality. Canfora et al.[34]has studied on a genetically modified plantsBrassicanapusand evaluated its effect on soil microbial diversity. Pablo et al.[35]researched another plant calledAcaciadealbata, they investigated the effect on soil microbial community over a chronological sequence as the plant invasion. They concluded that theA.dealbatamodified the structure of fungal and microbial communities; the fungal richness, density and diversity were altered inA.dealbatasoils. Zhao et al.[36]researched the variety of microbial diversity of vertical-flow constructed wetlands as the plant development and indicated that the development of the plant had a great effect on microbial community diversity. Prakash et al.[37]focused on the relationship between marine plants and their attached microbial. Four marine plants, two seaweed and two sea grass species were selected to screen their antimicrofouling activity, indicated that the crude acetone extract ofS.furcellatumexhibited the good antimicrofouling activity over the other marine plants.

There is still another point that needs to be mentioned, some studies focused on the metabolism of microbes or plants such as extracellular polymeric substances (EPS), antimicrobial molecules and plant extracts, utilized the changes of metabolites to discuss their effects on the other organisms. The changes of microbial or plants metabolites could characterize the changes of microbial diversity indirectly and have influence on other organisms, because different microbes or plants could secreted different metabolites, the same species of microbe could secreted different metabolites in different growth stages, it also secreted different metabolites in different environments. The following articles are research in this aspect. Wilson et al.[38]studied on the diversity of antimicrobial molecules secreted from the bacteria in marine biofilms and concluded that surface attached marine bacteria can target their antimicrobial activity towards competing bacteria in biofilms. Passarelli et al.[39]aimed to assess how the EPS compositions are related to microbial assemblages and they gave the conclusions that the changes in EPS composition were not only fully explained by modifications of microbial assemblages but also depended on the processes taking place in sediments and on environmental conditions. These variations of EPS compositions are likely to alter different ecosystem processes such as biostabilisation or pollutants trapping. Arora et al.[40]accounted the activity of antibacterial molecules of microorganisms for pathogen removal and they found that the investigation of the antibacterial molecules activity of the isolated microbial species is crucial to understand the mechanism behind pathogen removal. Peters et al.[41]extracted the antibacterial properties from the internal egg matrix, they confirmed the antibacterial properties were derived from one bacterial epibiontB.psychroduranshaving the competitive interactions with other organisms in the biofilms. Negi.[42]reviewed the various antimicrobial phytochemicals present in plant extracts, these antimicrobial phytochemicals could affect the microbial diversity, and they could prohibit the growth of pathogenic for food application.

2.4 Comparison of microbial diversity in different environments

Making the comparative research of microbial diversity in different circumstance or the different stages or status in the same surrounding is another popular research topic. It could be obtained that the variation regularity and the responses of the microbes in different conditions by comparison. This is an important way to investigate the relationships between microorganisms and the environments. Brahmaiah et al.[43]considered the microbial diversity in pretreating mixed anaerobic communities from different sources. The conclusion indicated among all the treatment methods examined, the method of long chain fatty acids showed higher microbial diversity. Luo et al.[44]compared the microbial diversity in the environments of black shale and stromatolite facies in the Mesoproterozoic Xiamaling Formation. Li et al.[45]studied the microbial diversity in different functional zones of continuous aerobic-anaerobic coupled process for sludgeinsitureduction and identified the bacteria responsible for COD & TN removal. Ashhab et al.[46]discussed the microbial community composition in biofouling of reverse-osmosis (RO) membranes under different shear rates during tertiary wastewater desalination and they found that more persistent bacteria grow on RO membranes under high shear rate. Zhao et al.[47]discussed the bacterial community variation in constructed wetlands with different types of plants; the data indicated that microbial mechanism of triclosan of 60 μg/L had a negative effect on bacterial abundance, community structure and function of constructed wetlands. This influence varied with the species of wetland plants. Epelde et al.[48]investigated the influence of sources of environmental degradation on microbial community dynamics in non-polluted and metal-polluted soils and got the conclusion that activity and biomass parameters are more sensitive than diversity parameters in different environments.

2.5 Discussion of the microbial diversity in microbial fuel cells (MFCs)

Bacterial-derived electricity has been known for more than one hundred years[49]. Since then, it took several decades to demonstrate that bacteria could carry out the "extracellular electron transfer" process without the aid of exogenous mediators[50-51]. Now, microbial fuel cells (MFCs) is a hotspot direction in the research field of microbiology, it is also a promising technology that harnesses the power of microorganisms to minimize environmental pollution and at the same time generate renewable electricity[52-54]. The composition of microbial community on a fuel cell decided its properties and efficiency, so researchers need to study microbial community in MFCs. Stratford et al.[55]considered microbial community diversity as a predictor of the power output of MFCs, there is a correlation between microbial consortia diversity and electrical output. Katuri et al.[56]analyzed the microbial diversity of anodic biofilm in a MFC using slaughterhouse wastewater, the results indicated that in MFC reactors, functionally stable electroactive bacteria are enriched under 100 Ω load compared to high resistance control conditions, and were able to sustain higher power in MFCs.Li et al.[57]investigated two conductive polymer materials which used to modify carbon felt anode, there arose a different microbial community with one polymer and the microbial diversity is adjusted. Quan et al.[58]studied the microbial community diversity under anode aeration of an air-cathode MFC, the result suggested that aeration caused a decline in anode microbial diversity, but the air-cathode MFC showed a good resistance to oxygen and demonstrated the potential to generate electricity under anoxic and aerobic conditions. Miroliaei et al.[59]investigated the effect of diversity cultures byE.coliandShewanellasp., and their combined on MFC performance. The result proved the type of strains has a great influence on the proportion and rate of electrons transferred.

2.6 Crossover study in different environment

Crossover study is an effective way to enhance the depth of the research. Using microbial diversity as a bridge, the connection between the different environment could be described better.

From the data above (Fig.4), most of the research was focused on the interaction study of water and soil. Tian et al.[60]studied the effects of long time drip-irrigation with oil-polluted water on microorganisms in reed rhizospheric soils, they found that oil contaminants reduced the diversity to some degree, and changed the dominant flora of bacterial community. Wang et al.[61]discussed the effect of a changed temperature on the microbial community in a tea orchard soil under different water contents, the result indicated the microbial communities varied with temperature, soil moisture and incubation time. Feng et al.[62]using a simulated river bioreactor as its natural state and investigated the contaminated source water remediation. They revealed the step feeding process could increase the bacteria diversity and enhance denitrification from the simulated bioreactor. Sun et al.[63]investigated the diversity of microbial communities in sludge-amended soils; the results reflected the changes in functional diversity of the soil microbial communities in a particular eco-environment, like soil amended with sewage sludge. Zhao et al.[64]using a aerobic granular sludge sequencing bioreactor (GSBR) and studied the change of microbial diversity in operation. They found that the treatment processes have effects on the structure of microbial communities and The GSBR bioreactor offers bright prospects for the treatment of pharmaceuticals and personal care products (PPCPs) wastewater.Ma et al.[65]compared the Microbial communities in an anaerobic dynamic membrane bioreactor for bulk sludge wastewater and cake layer wastewater treatment. The result revealed high microbial diversity in the bulk sludge and cake layer,Bacteroides,Clostridiaandδ-proteobacteriawere the pioneers of colonization on membranes.

3 Conclusion

Through reviewing and summarizing the SCI literature in recent 3 years, it was listed some common research directions in the aspect of microbial diversity research. From the data acquired by SCI databases and analyses, most studies focused on single study, there has been less interactive study. But the influential scientific journals rarely accepted the articles with single research, because there a contribution to science is limited unless the study formed its own system or discovered new species. The research roughly summarized as follows: ① Focusing merely on the microbial diversity in a special environment cannot obtain the satisfactory results, because there is not much significance for only state the facts without further explore. Associating the microbial community diversity with microbial function diversity is a good way to clarify.②If compared the microbial diversity in the similar but different environment, the result could indicate the response between the microbes and the environment, this may be helpful to the research on environmental microbiology.③For future researches, scholars should investigate the interaction relationship between organisms elucidated the interaction between them or concentrate on the cross-over study of different research objects, this maybe have a significant impact on social and economic life and the level of the article will be further improved.

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兰州交通大学青年基金项目(2014011)

赵萌萌 女，副教授，在读博士。研究方向为微生物生理生化及应用研究。Tel：0931-4938793,E-mail:zhaomm80@163.com

近三年微生物多样性研究进展

赵萌萌， 薛林贵

(兰州交通大学 化学与生物工程学院 甘肃省极端环境微生物资源与工程重点实验室，甘肃 兰州 730070)

综述了近三年来微生物多样性研究领域的研究进展，对不同年份相关文章的数量、不同数据库中相关文章的数量以及作者倾向于选择的不同微生物多样性研究对象的相关文章的数量进行了统计。文中针对微生物多样性研究领域作者选择的不同研究重点进行了分类和归纳，并且对其研究结果进行了简要介绍。为研究者提供了近年来微生物多样性研究的大致框架，为研究对象的选择和研究重点的设定提供依据。

研究进展；微生物多样性；近三年

Q939.91

A

1005-7021(2016)02-0093-08

10.3969/j.issn.1005-7021.2016.02.016