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Special Issue "Microbial Ecology and Diversity"

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A special issue of Diversity (ISSN 1424-2818).

Deadline for manuscript submissions: closed (15 April 2013)

Special Issue Editors

Guest Editor
Dr. Kristen M. DeAngelis (Website)

Department of Microbiology, University of Massachusetts Amherst, 102 Morrill IV N, 639 N. Pleasant St., Amherst, MA 01003-9298, USA
Fax: +1 413 545 1578
Interests: microbial ecology of terrestrial ecosystems; effects of climate change stress on populations and communities; lignocellulose decomposition; plant-microbial interactions in the rhizosphere
Guest Editor
Prof. Dr. Susan Leschine (Website)

Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, 212 Morrill IV N, 639 N. Pleasant St., Amherst, MA 01003-9298, USA
Fax: +1 413 545 1578
Interests: microbial physiology and diversity; soil microbiology; cellulose decomposition; biofilms; role of digestive tract microbes in animal health

Special Issue Information

Dear Colleagues,

Microbes embody the vast diversity of life on Earth. The extensive physiological diversity of microbes has long been recognized through traditional cultivation-based methods; however, with the advent of molecular techniques for community analysis, estimates of richness have increased dramatically. New technologies and lower DNA sequencing costs have led to an explosion in sequence-based microbial community analyses such as metagenomics, revealing astonishing diversity. The challenge now is to tie this richness and complexity to ecosystem function. In their natural environments microbes interact with each other and often with plants and animals. Such interactions are essential for ecosystem function and may relate to plant and animal health, biogeochemical cycling, and numerous other processes. Defining the microbial role in ecosystem function is complicated in part because microbial functions feed back at many scales. At the single cell scale, microbes sense and respond to their environments. At the population-level, there are myriad chemical inter- and intra-species communications that control group behaviors. At the community scale, composition changes with environmental factors, altering nutrient pools and process rates. 
This “Microbial Ecology and Diversity” Special Issue focuses on linking richness and composition of complex microbial communities with ecosystem function. Questions to be addressed include: How are microbial community structures and function related? What interactions with the environment or with other organisms control microbial activity? What can be gained or lost from examining natural versus controlled, laboratory systems? With this in mind, we hope to advance understanding of interactions among members of these communities, with associated plants and animals, as well as with their environment.

Prof. Dr. Kristen M. DeAngelis
Prof. Dr. Susan Leschine
Guest Editors

Submission

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Diversity is an international peer-reviewed Open Access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 800 CHF (Swiss Francs).


Keywords

  • microbial ecology
  • microbial diversity
  • community analysis
  • community structure and function
  • sequence-based techniques
  • microbiome
  • phylogeny
  • biogeochemical cycles

Published Papers (8 papers)

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Research

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Open AccessArticle Preliminary Analysis of Life within a Former Subglacial Lake Sediment in Antarctica
Diversity 2013, 5(3), 680-702; doi:10.3390/d5030680
Received: 15 May 2013 / Revised: 5 July 2013 / Accepted: 8 August 2013 / Published: 6 September 2013
Cited by 7 | PDF Full-text (753 KB) | HTML Full-text | XML Full-text
Abstract
Since the first descriptions of Antarctic subglacial lakes, there has been a growing interest and awareness of the possibility that life will exist and potentially thrive in these unique and little known environments. The unusual combination of selection pressures, and isolation from [...] Read more.
Since the first descriptions of Antarctic subglacial lakes, there has been a growing interest and awareness of the possibility that life will exist and potentially thrive in these unique and little known environments. The unusual combination of selection pressures, and isolation from the rest of the biosphere, might have led to novel adaptations and physiology not seen before, or indeed to the potential discovery of relic populations that may have become extinct elsewhere. Here we report the first microbiological analysis of a sample taken from a former subglacial lake sediment in Antarctica (Lake Hodgson, on the Antarctic Peninsula). This is one of a number of subglacial lakes just emerging at the margins of the Antarctic ice sheet due to the renewed onset of deglaciation. Microbial diversity was divided into 23.8% Actinobacteria, 21.6% Proteobacteria, 20.2% Planctomycetes and 11.6% Chloroflexi, characteristic of a range of habitat types ( Overall, common sequences were neither distinctly polar, low temperature, freshwater nor marine). Twenty three percent of this diversity could only be identified to “unidentified bacterium”. Clearly these are diverse ecosystems with enormous potential. Full article
(This article belongs to the Special Issue Microbial Ecology and Diversity)
Open AccessArticle Examination of a Culturable Microbial Population from the Gastrointestinal Tract of the Wood-Eating Loricariid Catfish Panaque nigrolineatus
Diversity 2013, 5(3), 641-656; doi:10.3390/d5030641
Received: 22 May 2013 / Revised: 2 August 2013 / Accepted: 13 August 2013 / Published: 19 August 2013
Cited by 2 | PDF Full-text (1012 KB) | HTML Full-text | XML Full-text
Abstract
Fish play a critical role in nutrient cycling and organic matter flow in aquatic environments. However, little is known about the microbial diversity within the gastrointestinal tracts that may be essential in these degradation activities. Panaque nigrolineatus is a loricariid catfish found [...] Read more.
Fish play a critical role in nutrient cycling and organic matter flow in aquatic environments. However, little is known about the microbial diversity within the gastrointestinal tracts that may be essential in these degradation activities. Panaque nigrolineatus is a loricariid catfish found in the Neotropics that have a rare dietary strategy of consuming large amounts of woody material in its natural environment. As a consequence, the gastrointestinal (GI) tract of P. nigrolineatus is continually exposed to high levels of cellulose and other recalcitrant wood compounds and is, therefore, an attractive, uncharacterized system to study microbial community diversity. Our previous 16S rRNA gene surveys demonstrated that the GI tract microbial community includes phylotypes having the capacity to degrade cellulose and fix molecular nitrogen. In the present study we verify the presence of a resident microbial community by fluorescence microscopy and focus on the cellulose-degrading members by culture-based and 13C-labeled cellulose DNA stable-isotope probing (SIP) approaches. Analysis of GI tract communities generated from anaerobic microcrystalline cellulose enrichment cultures by 16S rRNA gene analysis revealed phylotypes sharing high sequence similarity to known cellulolytic bacteria including Clostridium, Cellulomonas, Bacteroides, Eubacterium and Aeromonas spp. Related bacteria were identified in the SIP community, which also included nitrogen-fixing Azospirillum spp. Our ability to enrich for specialized cellulose-degrading communities suggests that the P. nigrolineatus GI tract provides a favorable environment for this activity and these communities may be involved in providing assimilable carbon under challenging dietary conditions. Full article
(This article belongs to the Special Issue Microbial Ecology and Diversity)
Open AccessArticle Untangling the Genetic Basis of Fibrolytic Specialization by Lachnospiraceae and Ruminococcaceae in Diverse Gut Communities
Diversity 2013, 5(3), 627-640; doi:10.3390/d5030627
Received: 17 May 2013 / Revised: 21 June 2013 / Accepted: 26 June 2013 / Published: 9 August 2013
Cited by 30 | PDF Full-text (552 KB) | HTML Full-text | XML Full-text
Abstract
The Lachnospiraceae and Ruminococcaceae are two of the most abundant families from the order Clostridiales found in the mammalian gut environment, and have been associated with the maintenance of gut health. While they are both diverse groups, they share a common role [...] Read more.
The Lachnospiraceae and Ruminococcaceae are two of the most abundant families from the order Clostridiales found in the mammalian gut environment, and have been associated with the maintenance of gut health. While they are both diverse groups, they share a common role as active plant degraders. By comparing the genomes of the Lachnospiraceae and Ruminococcaceae with the Clostridiaceae, a more commonly free-living group, we identify key carbohydrate-active enzymes, sugar transport mechanisms, and metabolic pathways that distinguish these two commensal groups as specialists for the degradation of complex plant material. Full article
(This article belongs to the Special Issue Microbial Ecology and Diversity)
Open AccessArticle Aerobic Methanotrophs in Natural and Agricultural Soils of European Russia
Diversity 2013, 5(3), 541-556; doi:10.3390/d5030541
Received: 6 June 2013 / Revised: 26 June 2013 / Accepted: 10 July 2013 / Published: 31 July 2013
Cited by 4 | PDF Full-text (1259 KB) | HTML Full-text | XML Full-text
Abstract
Human activities such as land management and global warming have great impact on the environment. Among changes associated with the global warming, rising methane emission is a serious concern. Therefore, we assessed methane oxidation activity and diversity of aerobic methanotrophic bacteria in [...] Read more.
Human activities such as land management and global warming have great impact on the environment. Among changes associated with the global warming, rising methane emission is a serious concern. Therefore, we assessed methane oxidation activity and diversity of aerobic methanotrophic bacteria in eight soil types (both unmanaged and agricultural) distributed across the European part of Russia. Using a culture-independent approach targeting pmoA gene, we provide the first baseline data on the diversity of methanotrophs inhabiting most typical soil types. The analysis of pmoA clone libraries showed that methanotrophic populations in unmanaged soils are less diverse than in agricultural areas. These clone sequences were placed in three groups of, so far, uncultured methanotrophs: USC-gamma, cluster I, and pmoA/amoA cluster, which are believed to be responsible for atmospheric methane oxidation in upland soils. Agricultural soils harbored methanotrophs related to genera Methylosinus, Methylocystis, Methylomicrobium, Methylobacter, and Methylocaldum. Despite higher numbers of detected molecular operational taxonomic units (MOTUs), managed soils showed decreased methane oxidation rates as observed in both in situ and laboratory experiments. Our results also suggest that soil restoration may have a positive effect on methane consumption by terrestrial ecosystems. Full article
(This article belongs to the Special Issue Microbial Ecology and Diversity)
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Open AccessArticle Assessing the Diversity and Composition of Bacterial Communities across a Wetland, Transition, Upland Gradient in Macon County Alabama
Diversity 2013, 5(3), 461-478; doi:10.3390/d5030461
Received: 15 April 2013 / Revised: 29 May 2013 / Accepted: 21 June 2013 / Published: 3 July 2013
Cited by 3 | PDF Full-text (922 KB) | HTML Full-text | XML Full-text
Abstract
Wetlands provide essential functions to the ecosphere that range from water filtration to flood control. Current methods of evaluating the quality of wetlands include assessing vegetation, soil type, and period of inundation. With recent advances in molecular and bioinformatic techniques, measurement of [...] Read more.
Wetlands provide essential functions to the ecosphere that range from water filtration to flood control. Current methods of evaluating the quality of wetlands include assessing vegetation, soil type, and period of inundation. With recent advances in molecular and bioinformatic techniques, measurement of the structure and composition of soil bacterial communities have become an alternative to traditional methods of ecological assessment. The objective of the current study was to determine whether soil bacterial community composition and structure changed along a single transect in Macon County, AL. Proteobacteria were the most abundant phyla throughout the soils in the study (ranging from 42.1% to 49.9% of total sequences). Phyla Acidobacteria (37.4%) and Verrucomicrobia (7.0%) were highest in wetland soils, Actinobacteria (14.6%) was highest in the transition area, and Chloroflexi (1.6%) was highest in upland soils. Principle Components Analysis (relative abundance) and Principle Coordinates Analysis (PCoA) (Unifrac weighted metric) plots were generated, showing distinction amongst the ecosystem types through clustering by taxonomic abundance and Unifrac scores at 3% dissimilarity, respectively. Selected soil properties (soil organic carbon and phosphatase enzyme activity) also differed significantly in transition soil ecosystem types, while showing predominance in the wetland area. This study suggests that with further study the structure and composition of soil bacterial communities may eventually be an important indicator of ecological impact in wetland ecosystems. Full article
(This article belongs to the Special Issue Microbial Ecology and Diversity)
Open AccessArticle In Situ Ecophysiology of Microbial Biofilm Communities Analyzed by CMEIAS Computer-Assisted Microscopy at Single-Cell Resolution
Diversity 2013, 5(3), 426-460; doi:10.3390/d5030426
Received: 22 April 2013 / Revised: 15 May 2013 / Accepted: 27 May 2013 / Published: 25 June 2013
Cited by 3 | PDF Full-text (4591 KB) | HTML Full-text | XML Full-text
Abstract
This paper describes the utility of CMEIAS (Center for Microbial Ecology Image Analysis System) computer-assisted microscopy to extract data from accurately segmented images that provide 63 different insights into the ecophysiology of microbial populations and communities within biofilms and other habitats. Topics [...] Read more.
This paper describes the utility of CMEIAS (Center for Microbial Ecology Image Analysis System) computer-assisted microscopy to extract data from accurately segmented images that provide 63 different insights into the ecophysiology of microbial populations and communities within biofilms and other habitats. Topics include quantitative assessments of: (i) morphological diversity as an indicator of impacts that substratum physicochemistries have on biofilm community structure and dominance-rarity relationships among populations; (ii) morphotype-specific distributions of biovolume body size that relate microbial allometric scaling, metabolic activity and growth physiology; (iii) fractal geometry of optimal cellular positioning for efficient utilization of allocated nutrient resources; (iv) morphotype-specific stress responses to starvation, environmental disturbance and bacteriovory predation; (v) patterns of spatial distribution indicating positive and negative cell–cell interactions affecting their colonization behavior; and (vi) significant methodological improvements to increase the accuracy of color-discriminated ecophysiology, e.g., differentiation of cell viability based on cell membrane integrity, cellular respiratory activity, phylogenetically differentiated substrate utilization, and N-acyl homoserine lactone-mediated cell–cell communication by bacteria while colonizing plant roots. The intensity of these ecophysiological attributes commonly varies at the individual cell level, emphasizing the importance of analyzing them at single-cell resolution and the proper spatial scale at which they occur in situ. Full article
(This article belongs to the Special Issue Microbial Ecology and Diversity)
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Review

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Open AccessReview Culture-Independent Molecular Tools for Soil and Rhizosphere Microbiology
Diversity 2013, 5(3), 581-612; doi:10.3390/d5030581
Received: 6 May 2013 / Revised: 21 June 2013 / Accepted: 25 June 2013 / Published: 2 August 2013
Cited by 12 | PDF Full-text (565 KB) | HTML Full-text | XML Full-text
Abstract
Soil microbial communities play an important role in plant health and soil quality. Researchers have developed a wide range of methods for studying the structure, diversity, and activity of microbes to better understand soil biology and plant-microbe interactions. Functional microbiological analyses of [...] Read more.
Soil microbial communities play an important role in plant health and soil quality. Researchers have developed a wide range of methods for studying the structure, diversity, and activity of microbes to better understand soil biology and plant-microbe interactions. Functional microbiological analyses of the rhizosphere have given new insights into the role of microbial communities in plant nutrition and plant protection against diseases. In this review, we present the most commonly used traditional as well as new culture-independent molecular methods to assess the diversity and function of soil microbial communities. Furthermore, we discuss advantages and disadvantages of these techniques and provide a perspective on emerging technologies for soil microbial community profiling. Full article
(This article belongs to the Special Issue Microbial Ecology and Diversity)
Open AccessReview Up Against The Wall: The Effects of Climate Warming on Soil Microbial Diversity and The Potential for Feedbacks to The Carbon Cycle
Diversity 2013, 5(2), 409-425; doi:10.3390/d5020409
Received: 15 April 2013 / Revised: 27 April 2013 / Accepted: 17 May 2013 / Published: 3 June 2013
Cited by 6 | PDF Full-text (519 KB) | HTML Full-text | XML Full-text
Abstract
Earth’s climate is warming, and there is evidence that increased temperature alters soil C cycling, which may result in a self-reinforcing (positive), microbial mediated feedback to the climate system. Though soil microbes are major drivers of soil C cycling, we lack an [...] Read more.
Earth’s climate is warming, and there is evidence that increased temperature alters soil C cycling, which may result in a self-reinforcing (positive), microbial mediated feedback to the climate system. Though soil microbes are major drivers of soil C cycling, we lack an understanding of how temperature affects SOM decomposition. Numerous studies have explored, to differing degrees, the extent to which climate change may affect biodiversity. While there is ample evidence that community diversity begets ecosystem stability and resilience, we know of keystone species that perform functions whose effects far outweigh their relative abundance. In this paper, we first review the meaning of microbial diversity and how it relates to ecosystem function, then conduct a literature review of field-based climate warming studies that have made some measure of microbial diversity. Finally, we explore how measures of diversity may yield a larger, more complete picture of climate warming effects on microbial communities, and how this may translate to altered carbon cycling and greenhouse gas emissions. While warming effects seem to be ecosystem-specific, the lack of observable consistency between measures is due in some part to the diversity in measures of microbial diversity. Full article
(This article belongs to the Special Issue Microbial Ecology and Diversity)

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