Genetic diversity and community structure of soil bacteria in Chinese fir plantations

To explore the diversity of soil bacteria and changes in the bacterial community structure of Chinese fir plantations of different generations and developmental stages, the genetic diversity of soil bacteria was studied using the 454 sequencing technology. The results showed that the bacterial genetic diversity and community structure of Chinese fir plantation plots under monoculture planting and rotation planting practices were as follows: the Shannon diversity indices of first-generation young plantation of Chinese fir plantations (FYC), second-generation young plantation (SYC), and third-generation young plantation (TYC) initially decreased and then increased to 8.45, 8.1, and 8.43, respectively. Due to different management and tending measures, the phyla showing considerable differences in relative abundance were Cyanobacteria, Nitrospirae, Fibrobacteres, Thermotogae, and Planctomycetes. The bacterial genetic diversity and community structure of Chinese fir plantations at different developmental stages were as follows: the bacterial diversity and the number of operational taxonomic units (OTUs) decreased with increasing forest age; with the increasing forest age of Chinese fir, the bacteria with considerable differences in the relative abundance were Burkholderiales, Xanthomonadales, Ktedonobacteria, Nitrosomonadales, Anaerolineae, and Holophagae. The predominant bacteria of the Chinese fir plantations were Acidothermus, Bradyrhizobium, Lactococcus, Planctomyces, Sorangium, and Bryobacter.

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Contrasting Effects of Chinese Fir Plantations of Different Stand Ages on Soil Enzyme Activities and Microbial Communities

Forests ◽

10.3390/f10010011 ◽

2018 ◽

Vol 10 (1) ◽

pp. 11 ◽

Cited By ~ 7

Author(s):

Chaoqun Wang ◽

Lin Xue ◽

Yuhong Dong ◽

Lingyu Hou ◽

Yihui Wei ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Relative Abundance ◽

Enzyme Activities ◽

Soil Enzyme ◽

Chinese Fir ◽

Fungal Communities ◽

Stand Age ◽

Forest Age ◽

Soil Enzyme Activities

Soil enzymes and microbial communities are key factors in forest soil ecosystem functions and are affected by stand age. In this study, we studied soil enzyme activities, composition and diversity of bacterial and fungal communities and relevant physicochemical properties at 0–10 cm depth (D1), 10–20 cm depth (D2) and 20–30 cm depth (D3) soil layers in 3-(3a), 6-(6a), 12-(12a), 18-(18a), 25-(25a), 32-(32a) and 49-year-old (49a) Chinese fir plantations to further reveal the effects of stand age on soil biotic properties. Spectrophotometry and high-throughput sequencing was used to assess the soil enzyme activity and microbial community composition and diversity of Chinese fir plantation of different stand ages, respectively. We found that soil catalase activity increased as the stand age of Chinese fir plantations increased, whereas the activities of urease, sucrase and β-glucosidase in 12a, 18a and 25a were lower than those in 6a, 32a and 49a. Shannon and Chao1 indices of bacterial and fungal communities first decreased gradually from 6a to 18a or 25a and then increased gradually from 25a to 49a. Interestingly, the sucrase and β-glucosidase activities and the Shannon and Chao1 indices in 3a were all lower than 6a. We found that the relative abundance of dominant microbial phyla differed among stand ages and soil depths. The proportion of Acidobacteria first increased and then decreased from low forest age to high forest age, and its relative abundance in 12a, 18a and 25a were higher than 3a, 32a and 49a, but the proportion of Proteobacteria was opposite. The proportion of Ascomycota first decreased and then increased from 6a to 49a, and its relative abundance in 12a, 18a and 25a was lower than 3a, 6a, 32a and 49a. Our results indicate that soil enzyme activities and the richness and diversity of the microbial community are limited in the middle stand age (from 12a to 25a), which is important for developing forest management strategies to mitigate the impacts of degradation of soil biological activities.

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Aquatic and semi aquatic Hemiptera community of Sonebeel, the largest wetland of Assam, northeastern India

Journal of Threatened Taxa ◽

10.11609/jott.3440.10.13.12792-12799 ◽

2018 ◽

Vol 10 (13) ◽

pp. 12792-12799

Author(s):

Anupama Saha ◽

Susmita Gupta

Keyword(s):

Species Richness ◽

Pest Control ◽

Relative Abundance ◽

Species Distribution ◽

Diversity Indices ◽

Environmental Data ◽

Northeastern India ◽

Ecological Roles

Aquatic and semiaquatic Hemiptera bugs play significant ecological roles, and they are important indicators and pest control agents. Little information is currently available concerning its populations in southern Assam. This study assessed hemipterans in four sites of Sonebeel, the largest wetland in Assam (3458.12 ha at full storage level), situated in Karimganj District. The major inflow and outflow of the wetland are the rivers Singla and Kachua, respectively (the Kachua drains into the Kushiyara River). Samples were trapped with pond nets and were seasonally recorded. This study recorded a total of 28 species of aquatic and semiaquatic hemipterans belonging to 20 genera under nine families. Population, geographical and environmental data (e.g., rainfall) were used to assess the relative abundance of species, species richness and different diversity indices, and species distribution.

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Microbial community structure and trichloroethylene degradation in groundwater

Canadian Journal of Microbiology ◽

10.1139/w05-025 ◽

2005 ◽

Vol 51 (6) ◽

pp. 433-439 ◽

Cited By ~ 23

Author(s):

J A Humphries ◽

A M.H Ashe ◽

J A Smiley ◽

C G Johnston

Keyword(s):

Community Structure ◽

Clone Library ◽

Sequence Data ◽

Restriction Analysis ◽

Diversity Indices ◽

Department Of Energy ◽

Tetrazolium Chloride ◽

Degrading Bacteria ◽

Trichloroethylene Degradation ◽

Rdna Clone

Trichloroethylene (TCE) is a prevalent contaminant of groundwater that can be cometabolically degraded by indigenous microbes. Groundwater contaminated with TCE from a US Department of Energy site in Ohio was used to characterize the site-specific impact of phenol on the indigenous bacterial community for use as a possible remedial strategy. Incubations of14C-TCE-spiked groundwater amended with phenol showed increased TCE mineralization compared with unamended groundwater. Community structure was determined using DNA directly extracted from groundwater samples. This DNA was then analyzed by amplified ribosomal DNA restriction analysis. Unique restriction fragment length polymorphisms defined operational taxonomic units that were sequenced to determine phylogeny. DNA sequence data indicated that known TCE-degrading bacteria including relatives of Variovorax and Burkholderia were present in site water. Diversity of the amplified microbial rDNA clone library was lower in phenol-amended communities than in unamended groundwater (i.e., having Shannon–Weaver diversity indices of 2.0 and 2.2, respectively). Microbial activity was higher in phenol-amended ground water as determined by measuring the reduction of 2-(p-iodophenyl)-3(p-nitrophenyl)-5-phenyl tetrazolium chloride. Thus phenol amendments to groundwater correlated with increased TCE mineralization, a decrease in diversity of the amplified microbial rDNA clone library, and increased microbial activity.Key words: community structure, trichloroethylene, degradation, groundwater.

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Comparison of Microbiological Characteristics and Genetic Diversity between Burkholderia cepacia Complex Isolates from Vascular Access and Other Clinical Infections

Microorganisms ◽

10.3390/microorganisms9010051 ◽

2020 ◽

Vol 9 (1) ◽

pp. 51

Author(s):

Min Yi Wong ◽

Yuan-Hsi Tseng ◽

Tsung-Yu Huang ◽

Bor-Shyh Lin ◽

Chun-Wu Tung ◽

...

Keyword(s):

Genetic Diversity ◽

Vascular Access ◽

Burkholderia Cepacia ◽

Bacterial Species ◽

Diversity Indices ◽

Burkholderia Cepacia Complex ◽

Reca Gene ◽

Clinical Effects ◽

Environmental Distribution ◽

Microbiological Characteristics

Burkholderia cepacia complex (BCC) is a group of closely related bacteria with widespread environmental distribution. BCC bacteria are opportunistic pathogens that cause nosocomial infections in patients, especially cystic fibrosis (CF). Multilocus sequence typing (MLST) is used nowadays to differentiate species within the BCC complex. This study collected 41 BCC isolates from vascular access infections (VAIs) and other clinical infections between 2014 and 2020. We preliminarily identified bacterial isolates using standard biochemical procedures and further conducted recA gene sequencing and MLST for species identification. We determined genetic diversity indices using bioinformatics software. We studied 14 isolates retrieved from patients with VAIs and observed that Burkholderia cepacia was the predominant bacterial species, and B. contaminans followed by B. cenocepacia were mainly retrieved from patients with other infections. According to MLST data, we identified that all B. contaminans isolates belonged to ST102, while a wide variety of sequence types (STs) were found in B. cenocepacia isolates. In summary, the high diversity and easy transmission of BCC increase BCC infections, which provides insights into their potential clinical effects in non-CF infections.

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On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Genetics Selection Evolution ◽

10.1186/s12711-021-00639-w ◽

2021 ◽

Vol 53 (1) ◽

Author(s):

Gabriele Senczuk ◽

Salvatore Mastrangelo ◽

Paolo Ajmone-Marsan ◽

Zsolt Becskei ◽

Paolo Colangelo ◽

...

Keyword(s):

Genetic Diversity ◽

Diversity Indices ◽

Melting Pot ◽

Cattle Breeds ◽

Snp Data ◽

Early Migration ◽

Genome Wide ◽

European Colonization ◽

Approximate Bayesian ◽

European Cattle

Abstract Background During the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine cattle and local aurochs resulting in an exclusive pattern of genetic diversity. Among the most ancient European cattle are breeds that belong to the so-called Podolian trunk, the history of which is still not well established. Here, we used genome-wide single nucleotide polymorphism (SNP) data on 806 individuals belonging to 36 breeds to reconstruct the origin and diversification of Podolian cattle and to provide a reliable scenario of the European colonization, through an approximate Bayesian computation random forest (ABC-RF) approach. Results Our results indicate that European Podolian cattle display higher values of genetic diversity indices than both African taurine and Asian indicine breeds. Clustering analyses show that Podolian breeds share close genomic relationships, which suggests a likely common genetic ancestry. Among the simulated and tested scenarios of the colonization of Europe from taurine cattle, the greatest support was obtained for the model assuming at least two waves of diffusion. Time estimates are in line with an early migration from the domestication centre of non-Podolian taurine breeds followed by a secondary migration of Podolian breeds. The best fitting model also suggests that the Italian Podolian breeds are the result of admixture between different genomic pools. Conclusions This comprehensive dataset that includes most of the autochthonous cattle breeds belonging to the so-called Podolian trunk allowed us not only to shed light onto the origin and diversification of this group of cattle, but also to gain new insights into the diffusion of European cattle. The most well-supported scenario of colonization points to two main waves of migrations: with one that occurred alongside with the Neolithic human expansion and gave rise to the non-Podolian taurine breeds, and a more recent one that favoured the diffusion of European Podolian. In this process, we highlight the importance of both the Mediterranean and Danube routes in promoting European cattle colonization. Moreover, we identified admixture as a driver of diversification in Italy, which could represent a melting pot for Podolian cattle.

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Genetic melting pot and importance of long-distance dispersal indicated in the Gladiolus imbricatus L. populations in the Polish Carpathians

Scientific Reports ◽

10.1038/s41598-021-96135-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Agnieszka Sutkowska ◽

Józef Mitka ◽

Tomasz Warzecha ◽

Jakub Bunk ◽

Julia Rutkowska ◽

...

Keyword(s):

Genetic Diversity ◽

Diversity Indices ◽

Western Carpathians ◽

Genetic Structuring ◽

Long Distance ◽

Plant Populations ◽

Genetic Stock ◽

Melting Pot ◽

Mountain Ranges ◽

Eastern Carpathians

AbstractThe genetic diversity in 11 populations of Gladiolus imbricatus in five mountain ranges, including the Tatra, Pieniny, Gorce, Beskid Niski (Western Carpathians) and Bieszczady Mts (Eastern Carpathians), was studied with inter-simple sequence repeat (ISSR) markers. The species is a perennial plant occurring in open and semi-open sites of anthropogenic origin (meadows and forest margins). We checked a hypothesis on the microrefugial character of the plant populations in the Pieniny Mts, a small calcareous Carpathian range of complicated relief that has never been glaciated. Plant populations in the Tatra and Pieniny Mts had the highest genetic diversity indices, pointing to their long-term persistence. The refugial vs. the non-refugial mountain ranges accounted for a relatively high value of total genetic variation [analysis of molecular variance (AMOVA), 14.12%, p = 0.003]. One of the Pieniny populations was of hybridogenous origin and shared genetic stock with the Tatra population, indicating there is a local genetic melting pot. A weak genetic structuring of populations among particular regions was found (AMOVA, 4.5%, p > 0.05). This could be an effect of the frequent short-distance and sporadic long-distance gene flow. The dispersal of diaspores between the remote populations in the Western Carpathians and Eastern Carpathians could be affected by the historical transportation of flocks of sheep from the Tatra to Bieszczady Mts.

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The use of diversity indices for local assessment of marine sediment quality

Scientific Reports ◽

10.1038/s41598-021-94636-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Shinya Hosokawa ◽

Kyosuke Momota ◽

Anthony A. Chariton ◽

Ryoji Naito ◽

Yoshiyuki Nakamura

Keyword(s):

Community Structure ◽

Sample Size ◽

Small Sample Size ◽

Benthic Communities ◽

Sediment Quality ◽

Diversity Indices ◽

Small Sample ◽

Species Density ◽

Local Case ◽

Two Indices

AbstractDiversity indices are commonly used to measure changes in marine benthic communities. However, the reliability (and therefore suitability) of these indices for detecting environmental change is often unclear because of small sample size and the inappropriate choice of communities for analysis. This study explored uncertainties in taxonomic density and two indices of community structure in our target region, Japan, and in two local areas within this region, and explored potential solutions. Our analysis of the Japanese regional dataset showed a decrease in family density and a dominance of a few species as sediment conditions become degraded. Local case studies showed that species density is affected by sediment degradation at sites where multiple communities coexist. However, two indices of community structure could become insensitive because of masking by community variability, and small sample size sometimes caused misleading or inaccurate estimates of these indices. We conclude that species density is a sensitive indicator of change in marine benthic communities, and emphasise that indices of community structure should only be used when the community structure of the target community is distinguishable from other coexisting communities and there is sufficient sample size.

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Mitochondrial Genetic Diversity among Farmed Stocks of Oreochromis spp. (Perciformes, Cichlidae) in Madagascar

Diversity ◽

10.3390/d13070281 ◽

2021 ◽

Vol 13 (7) ◽

pp. 281

Author(s):

Nicolas Hubert ◽

Elodie Pepey ◽

Jean-Michel Mortillaro ◽

Dirk Steinke ◽

Diana Edithe Andria-Mananjara ◽

...

Keyword(s):

Genetic Diversity ◽

Low Income ◽

Food System ◽

Production Systems ◽

Dna Barcode ◽

Diversity Indices ◽

Low Income Countries ◽

Wild Populations ◽

Fast Development ◽

Well Differentiated

The fast development of aquaculture over the past decades has made it the main source of fish protein and led to its integration into the global food system. Mostly originating from inland production systems, aquaculture has emerged as strategy to decrease malnutrition in low-income countries. The Nile tilapia (Oreochromis niloticus) was introduced to Madagascar in the 1950s, and is now produced nationally at various scales. Aquaculture mostly relies on fry harvested from wild populations and grow-out in ponds for decades. It has recently been diversified by the introduction of several fast-growing strains. Little is known how local genetic diversity compares to recently introduced strains, although high and comparable levels of genetic diversity have previously been observed for both wild populations and local stocks. Our study compares DNA barcode genetic diversity among eight farms and several strains belonging to three species sampled. DNA-based lineage delimitation methods were applied and resulted in the detection of six well differentiated and highly divergent lineages. A comparison of DNA barcode records to sequences on the Barcode of Life Data System (BOLD) helped to trace the origin of several of them. Both haplotype and nucleotide diversity indices highlight high levels of mitochondrial genetic diversity, with several local strains displaying higher diversity than recently introduced strains. This allows for multiple options to maintain high levels of genetic diversity in broodstock and provides more options for selective breeding programs.

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Archaeal ammonia oxidizers respond to soil factors at smaller spatial scales than the overall archaeal community does in a high Arctic polar oasis

Canadian Journal of Microbiology ◽

10.1139/cjm-2015-0669 ◽

2016 ◽

Vol 62 (6) ◽

pp. 485-491 ◽

Cited By ~ 3

Author(s):

Samiran Banerjee ◽

Nabla Kennedy ◽

Alan E. Richardson ◽

Keith N. Egger ◽

Steven D. Siciliano

Keyword(s):

Community Structure ◽

Spatial Scales ◽

Archaeal Community ◽

Diversity Indices ◽

High Arctic ◽

Total Carbon ◽

Spatial Dependency ◽

Edaphic Factors ◽

Total Carbon Content ◽

Arctic Soils

Archaea are ubiquitous and highly abundant in Arctic soils. Because of their oligotrophic nature, archaea play an important role in biogeochemical processes in nutrient-limited Arctic soils. With the existing knowledge of high archaeal abundance and functional potential in Arctic soils, this study employed terminal restriction fragment length polymorphism (t-RFLP) profiling and geostatistical analysis to explore spatial dependency and edaphic determinants of the overall archaeal (ARC) and ammonia-oxidizing archaeal (AOA) communities in a high Arctic polar oasis soil. ARC communities were spatially dependent at the 2–5 m scale (P < 0.05), whereas AOA communities were dependent at the ∼1 m scale (P < 0.0001). Soil moisture, pH, and total carbon content were key edaphic factors driving both the ARC and AOA community structure. However, AOA evenness had simultaneous correlations with dissolved organic nitrogen and mineral nitrogen, indicating a possible niche differentiation for AOA in which dry mineral and wet organic soil microsites support different AOA genotypes. Richness, evenness, and diversity indices of both ARC and AOA communities showed high spatial dependency along the landscape and resembled scaling of edaphic factors. The spatial link between archaeal community structure and soil resources found in this study has implications for predictive understanding of archaea-driven processes in polar oases.

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Environmental Sequencing Provides Reasonable Estimates of the Relative Abundance of Specific Picoeukaryotes

Applied and Environmental Microbiology ◽

10.1128/aem.00560-16 ◽

2016 ◽

Vol 82 (15) ◽

pp. 4757-4766 ◽

Cited By ~ 55

Author(s):

Caterina R. Giner ◽

Irene Forn ◽

Sarah Romac ◽

Ramiro Logares ◽

Colomban de Vargas ◽

...

Keyword(s):

Microbial Diversity ◽

High Throughput ◽

Relative Abundance ◽

Ribosomal Dna ◽

18S Rdna ◽

High Throughput Sequencing ◽

454 Sequencing ◽

Epifluorescence Microscopy ◽

Environmental Sequencing

ABSTRACTHigh-throughput sequencing (HTS) is revolutionizing environmental surveys of microbial diversity in the three domains of life by providing detailed information on which taxa are present in microbial assemblages. However, it is still unclear how the relative abundance of specific taxa gathered by HTS correlates with cell abundances. Here, we quantified the relative cell abundance of 6 picoeukaryotic taxa in 13 planktonic samples from 6 European coastal sites using epifluorescence microscopy on tyramide signal amplification-fluorescencein situhybridization preparations. These relative abundance values were then compared with HTS data obtained in three separate molecular surveys: 454 sequencing of the V4 region of the 18S ribosomal DNA (rDNA) using DNA and RNA extracts (DNA-V4 and cDNA-V4) and Illumina sequencing of the V9 region (cDNA-V9). The microscopic and molecular signals were generally correlated, indicating that a relative increase in specific 18S rDNA was the result of a large proportion of cells in the given taxa. Despite these positive correlations, the slopes often deviated from 1, precluding a direct translation of sequences to cells. Our data highlighted clear differences depending on the nucleic acid template or the 18S rDNA region targeted. Thus, the molecular signal obtained using cDNA templates was always closer to relative cell abundances, while the V4 and V9 regions gave better results depending on the taxa. Our data support the quantitative use of HTS data but warn about considering it as a direct proxy of cell abundances.IMPORTANCEDirect studies on marine picoeukaryotes by epifluorescence microscopy are problematic due to the lack of morphological features and due to the limited number and poor resolution of specific phylogenetic probes used in fluorescencein situhybridization (FISH) routines. As a consequence, there is an increasing use of molecular methods, including high-throughput sequencing (HTS), to study marine microbial diversity. HTS can provide a detailed picture of the taxa present in a community and can reveal diversity not evident using other methods, but it is still unclear what the meaning of the sequence abundance in a given taxon is. Our aim is to investigate the correspondence between the relative HTS signal and relative cell abundances in selected picoeukaryotic taxa. Environmental sequencing provides reasonable estimates of the relative abundance of specific taxa. Better results are obtained when using RNA extracts as the templates, while the region of 18S ribosomal DNA had different influences depending on the taxa assayed.

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