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Diversity, Volume 5, Issue 3 (September 2013), Pages 426-702

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Research

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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 include
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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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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 4 | 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 the
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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 A Simple Sequence Repeat (SSR) Marker Comparison of a Large In- and Ex-situ Potato Landrace Cultivar Collection from Peru Reaffirms the Complementary Nature of both Conservation Strategies
Diversity 2013, 5(3), 505-521; doi:10.3390/d5030505
Received: 24 April 2013 / Revised: 19 June 2013 / Accepted: 21 June 2013 / Published: 10 July 2013
Cited by 3 | PDF Full-text (988 KB) | HTML Full-text | XML Full-text
Abstract
An enhanced understanding of the temporal dynamics of intraspecific diversity is anticipated to improve the adequacy of conservation priorities, methods and metrics. We report on the comparative genetic composition of ex- and in-situ landrace cultivar populations from a potato diversity hotspot in the
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An enhanced understanding of the temporal dynamics of intraspecific diversity is anticipated to improve the adequacy of conservation priorities, methods and metrics. We report on the comparative genetic composition of ex- and in-situ landrace cultivar populations from a potato diversity hotspot in the Andes. A total of 989 landrace cultivars belonging to contemporary custodian-farmer in situ collections from central Peru were compared with 173 accessions from a spatially analogous, but temporally differential ex situ composite genotype reference (CGR) set using 15 nuclear microsatellite markers. A total of 173 alleles were detected, with 129 alleles (74.6%) being shared between both populations. Both populations contain exclusive allelic diversity with 32 and 12 unique alleles belonging to the ex- and in-situ population, respectively. The mean unbiased expected heterozygosity values of the ex- and in-situ population are very similar, 0.749 versus 0.727, with a slightly wider range and standard deviation encountered for the in situ population. Analysis of Molecular Variance shows that 98.8% of the total variation is found within both populations, while the fixation index (Fst = 0.01236) corroborates that the populations are not well differentiated. Surprisingly, only 41.0% of the ex situ population encounters a similar landrace cultivar in 23.4% of the in situ population at a non-stringent threshold similarity coefficient of 0.80. While the ex- and in-situ population under comparison show similarities and unique features at the allelic level, their landrace cultivar composition is surprisingly distinct. Results affirm that crop evolution is an ongoing phenomenon and that change in fixed geographies is occurring. Full article
(This article belongs to the Special Issue Genetic Diversity and Molecular Evolution)
Open AccessArticle Regional Conservation Status of Scleractinian Coral Biodiversity in the Republic of the Marshall Islands
Diversity 2013, 5(3), 522-540; doi:10.3390/d5030522
Received: 5 April 2013 / Revised: 1 July 2013 / Accepted: 3 July 2013 / Published: 18 July 2013
Cited by 1 | PDF Full-text (1541 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Preventing the loss of biodiversity is a major challenge in mega-diverse ecosystems such as coral reefs where there is a critical shortage of baseline demographic data. Threatened species assessments play a valuable role in guiding conservation action to manage and mitigate biodiversity loss,
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Preventing the loss of biodiversity is a major challenge in mega-diverse ecosystems such as coral reefs where there is a critical shortage of baseline demographic data. Threatened species assessments play a valuable role in guiding conservation action to manage and mitigate biodiversity loss, but they must be undertaken with precise information at an appropriate spatial scale to provide accurate classifications. Here we explore the regional conservation status of scleractinian corals on isolated Pacific Ocean atolls in the Republic of the Marshall Islands. We compile an integrated regional species list based upon new and historical records, and compare how well the regional threat classifications reflect species level priorities at a global scale. A similar proportion of the 240 species of hard coral recorded in the current survey are classified as Vulnerable at the regional scale as the global scale using the International Union for the Conservation of Nature (IUCN) Red List criteria (23% and 20% respectively), however there are distinct differences in the composition of species. When local abundance data is taken into account, a far greater proportion of the regional diversity (up to 80%) may face an elevated risk of local extinction. These results suggest coral communities on isolated Pacific coral reefs, which are often predicted to be at low risk, are still vulnerable due to the small and fragmented nature of their populations. This reinforces that to adequately protect biodiversity, ongoing threatened species monitoring and the documentation of species-level changes in abundance and distribution is imperative. Full article
(This article belongs to the Special Issue Marine Biodiversity)
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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 5 | 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 eight
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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 Loss of European Dry Heaths in NW Spain: A Case Study
Diversity 2013, 5(3), 557-580; doi:10.3390/d5030557
Received: 13 May 2013 / Revised: 21 June 2013 / Accepted: 16 July 2013 / Published: 2 August 2013
Cited by 3 | PDF Full-text (2295 KB) | HTML Full-text | XML Full-text
Abstract
Natural habitats are continuing to deteriorate in Europe with an increasing number of wild species which are also seriously threatened. Consequently, a coherent European ecological network (Natura 2000) for conservation of natural habitats and the wild fauna and flora (Council Directive 92/43/EEC) was
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Natural habitats are continuing to deteriorate in Europe with an increasing number of wild species which are also seriously threatened. Consequently, a coherent European ecological network (Natura 2000) for conservation of natural habitats and the wild fauna and flora (Council Directive 92/43/EEC) was created. Even so, there is currently no standardized methodology for surveillance and assessment of habitats, a lack that it is particularly problematic for those habitats occupying large areas (heathlands, forests, dunes, wetlands) and which require a great deal of effort to be monitored. In this paper we evaluate the changes affecting the European dry heaths (Nat-2000 4030) from the SCI Os Ancares–O Courel (Galicia, NW Spain) during the past decade. High-resolution aerial imagery analyses and Geographic Information Systems (GIS) were used. Losses of more than 7,000 ha (20.3%) of European dry heaths were computed during the 2003–2011 period in the SCI Os Ancares–O Courel, and also an increase of the degree of fragmentation was demonstrated for this habitat. Paradoxically, major impacts (afforestations, pasturelands) were financed by agri-environmental funds from the EU. Rather than promote biodiversity, these activities have provoked serious damages in this habitat of community interest, which is in complete opposition to the objectives of protection involved in the declaration of the SCI Os Ancares–O Courel. Full article
(This article belongs to the Special Issue Biodiversity Loss & Habitat Fragmentation)
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Open AccessArticle A Proposed Revision of Diversity Measures
Diversity 2013, 5(3), 613-626; doi:10.3390/d5030613
Received: 3 July 2013 / Revised: 13 July 2013 / Accepted: 22 July 2013 / Published: 9 August 2013
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Abstract
The current measures of diversity for vegetation, namely alpha, beta, and gamma diversity are not logically consistent, which reduces their effectiveness as a framework for comparative vegetation analysis. The current terms mix concepts: specifically, while alpha diversity measures floristic diversity at a site,
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The current measures of diversity for vegetation, namely alpha, beta, and gamma diversity are not logically consistent, which reduces their effectiveness as a framework for comparative vegetation analysis. The current terms mix concepts: specifically, while alpha diversity measures floristic diversity at a site, and gamma diversity measures floristic diversity regionally, beta diversity is a measure of diversity between two sites and measures a different phenomenon. We seek to rationalise measures of diversity providing a scalar set of measures. Our approach recognises vegetation diversity extends beyond species diversity and should include the various ways plants express themselves phenotypically. We propose four types of diversity, with a new set of prefixes: Type 1 diversity = the largest scale−the regional species pool; Type 2 diversity = the large habitat scale−where species in a habitat have been selected from the regional species pool; Type 3 diversity = intra-habitat expression of floristics, structure, and physiognomy; and Type 4 diversity = the finest scale of expression of vegetation diversity reflecting site selection of floristics, physiography, and phenotypic expression and reproductive strategy. This proposed framework adds significant new power to measures of diversity by extending the existing components to cover floristics, structure, physiognomy, and other forms of phenotypic expression. Full article
(This article belongs to the Special Issue Biogeography and Biodiversity Conservation)
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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 40 | 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 as
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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 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
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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 in
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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 Genetic Diversity of Black Salamanders (Aneides flavipunctatus) across Watersheds in the Klamath Mountains
Diversity 2013, 5(3), 657-679; doi:10.3390/d5030657
Received: 31 May 2013 / Revised: 2 August 2013 / Accepted: 8 August 2013 / Published: 29 August 2013
Cited by 3 | PDF Full-text (8134 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Here we characterize the genetic structure of Black Salamanders (Aneides flavipunctatus) in the Klamath Mountains of northwestern California and southwestern Oregon using mitochondrial and nuclear DNA sequences. We hypothesized that the Sacramento, Smith, Klamath, and Rogue River watersheds would represent distinct
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Here we characterize the genetic structure of Black Salamanders (Aneides flavipunctatus) in the Klamath Mountains of northwestern California and southwestern Oregon using mitochondrial and nuclear DNA sequences. We hypothesized that the Sacramento, Smith, Klamath, and Rogue River watersheds would represent distinct genetic populations based on prior ecological results, which suggest that Black Salamanders avoid high elevations such as the ridges that separate watersheds. Our mitochondrial results revealed two major lineages, one in the Sacramento River watershed, and another containing the Klamath, Smith, and Rogue River watersheds. Clustering analyses of our thirteen nuclear loci show the Sacramento watershed population to be genetically distinctive. Populations in the Klamath, Smith, and Rogue watersheds are also distinctive but not as differentiated and their boundaries do not correspond to watersheds. Our historical demographic analyses suggest that the Sacramento population has been isolated from the Klamath populations since the mid-Pleistocene, with negligible subsequent gene flow (2 Nm ≤ 0.1). The Smith and Rogue River watershed populations show genetic signals of recent population expansion. These results suggest that the Sacramento River and Klamath River watersheds served as Pleistocene refugia, and that the Rogue and Smith River watersheds were colonized more recently by northward range expansion from the Klamath. Full article
(This article belongs to the Special Issue Genetic Diversity and Molecular Evolution)
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 8 | 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 the
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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)

Review

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Open AccessReview Can Climate Change Trigger Massive Diversity Cascades in Terrestrial Ecosystems?
Diversity 2013, 5(3), 479-504; doi:10.3390/d5030479
Received: 3 May 2013 / Revised: 8 June 2013 / Accepted: 13 June 2013 / Published: 5 July 2013
Cited by 5 | PDF Full-text (630 KB) | HTML Full-text | XML Full-text
Abstract
We summarize research on diversity and trophic interactions under a trophic cascades model that is reframed and expanded from the traditional biomass- or abundance- based indirect effects and discuss the response of such “diversity cascades” to climate change and other global change parameters.
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We summarize research on diversity and trophic interactions under a trophic cascades model that is reframed and expanded from the traditional biomass- or abundance- based indirect effects and discuss the response of such “diversity cascades” to climate change and other global change parameters. The studies we summarize encompass dynamic processes in which species richness or evenness in one trophic level indirectly affects or is affected by changes in a non-adjacent level. The diversity cascade concept explicitly links trophic cascades models to the debates about biodiversity loss, exotic species gain, ecosystem services and biological control. First, we summarize the idea that the trophic cascades model includes different currencies and alternative processes. Second, we question the paradigm that trophic cascades weaken as the complexity of the community increases. Third, we illustrate the mechanisms by which diversity cascades may follow indirect bottom-up and top-down pathways. Fourth, we show how this diversity cascades model has been applied successfully to frame questions in conservation, agriculture and infectious disease. Finally, we examine the implications of diversity cascades for our understanding of how climate change affects biodiversity and call for an increase in the scope of experiments and focused hypotheses on indirect trophic effects and how these processes may lead to very large changes in biodiversity. Full article
(This article belongs to the Special Issue Tropical Forests Ecology and Climate Change)
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 17 | 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 the
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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)

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