The biogeography of fungal communities in wetland sediments along the Changjiang River and other sites in China

Wu, Ben‐Lai; Tian, Jianqing; Bai, Chun-Ming; Xiang, Meichun; Sun, Jingzu; Liu, Xingzhong

doi:10.1038/ismej.2013.29

Cited by 94 publications

(84 citation statements)

References 53 publications

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“…A 1,000-cross-validation process was used to decrease the structure complexity of the MRT. Predictive accuracy was estimated from the crossvalidated relative error, which varies from 0 for a perfect tree to close to 1 for a poor tree (8). MRT analysis was carried out with the package mvpart in the R statistical programming environment.…”

Section: Methodsmentioning

confidence: 99%

“…For example, it has been well documented for plant and animal communities that community similarity decreased with geographic distance, known as the distance-decay relationship (3, 4). In recent years, a number of studies have been conducted to investigate biogeographic patterns of microorganisms, including bacteria, archaea, fungi, and other microbial eukaryotes (3,(5)(6)(7)(8)(9)(10). A growing body of research has shown that microorganisms, like plants and animals, exhibited distance-decay patterns in different habitats at various taxonomic resolutions (2,3,(11)(12)(13)(14)(15)(16)(17)(18).…”

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confidence: 99%

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Distance-Decay Relationship for Biological Wastewater Treatment Plants

Wang

Wen

Deng

et al. 2016

Appl Environ Microbiol

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Patterns in the spatial distribution of organisms provide important information about mechanisms underlying biodiversity and the complexity of ecosystems. One of the most well-documented spatial patterns is the distance-decay relationship, which is a universal biogeographic pattern observed repeatedly for plant and animal communities, particularly for microorganisms in natural ecosystems such as soil, ocean, and salt marsh sediment. However, it is uncertain whether the microorganisms exhibit a distance-decay pattern in engineered ecosystems. Therefore, we measured the distance-decay relationship across various microbial functional and phylogenetic groups in 26 biological wastewater treatment plants (WWTPs) in China using a functional gene array (GeoChip 4.2). We found that microbial communities of activated sludge in WWTPs exhibited a significant but very weak distance-decay relationship. The taxon-area z values for different functional and phylogenetic groups were <0.0065, which is about 1 to 2 orders of magnitude lower than those observed in microbial communities elsewhere. Variation-partitioning analysis (VPA) showed that the relationships were driven by both environmental heterogeneity and geographic distance. Collectively, these results provided new insights into the spatial scaling of microbial communities in engineering ecosystems and highlighted the importance of environmental heterogeneity and geographic distance in shaping biogeographic patterns. IMPORTANCEDetermining the distance-decay relationship of microbial biodiversity is important but challenging in microbial ecology. All studies to date are based on natural environments; thus, it remains unclear whether there is such a relationship in an engineered ecosystem. The present study shows that there is a very weak distance-decay relationship in an engineered ecosystem (WWTPs) at the regional-to-continental scale. This study makes fundamental contributions to a mechanistic, predictive understanding of microbial biogeography.A central goal of ecology is to understand how biodiversity is generated and maintained (1). Spatial patterns of species diversity offer insights into the mechanisms shaping biodiversity and are of practical importance for predicting the risk of biodiversity loss by environmental changes and consequently for setting up conservation priorities (2). Therefore, the spatial distribution patterns of species diversity have solicited substantial attention. Traditionally, the field of spatial distribution patterns of biodiversity has focused on plants and animals. For example, it has been well documented for plant and animal communities that community similarity decreased with geographic distance, known as the distance-decay relationship (3, 4). In recent years, a number of studies have been conducted to investigate biogeographic patterns of microorganisms, including bacteria, archaea, fungi, and other microbial eukaryotes (3,(5)(6)(7)(8)(9)(10). A growing body of research has shown that microorganisms, like plants and animals, exh...

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Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

Distance-Decay Relationship for Biological Wastewater Treatment Plants

Wang

Wen

Deng

et al. 2016

Appl Environ Microbiol

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“…Comparatively speaking, there seemed a greater proportion of fungal OTUs belonging to the resident group in the marine environment than in fresh-water environments (Andreakis et al 2015;Wu et al 2013).…”

Section: Barcoding Aquatic Fungal Samplesmentioning

confidence: 97%

“…Using both culture-dependent and culture-independent (polymerase chain reaction followed by denaturing gradient gel electrophoresis (PCR-DGGE)) methods, Wu et al (2013) assessed the influence of historical and contemporary factors on the distributions of fungi in the sediments at 10 locations along the Changjiang River (the third-longest river in the world after the Nile and Amazon) and at 10 other freshwater locations in China. Interestingly, the culture-dependent approach coupled with ITS sequencing detected a greater species richness (a total 177 OTUs) than the PCR-DGGE analysis (145 OTUs).…”

Section: Barcoding Aquatic Fungal Samplesmentioning

confidence: 99%

Fungal DNA barcoding

2016

Genome

190

139

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Fungi are ubiquitous in both natural and human-made environments. They play important roles in the health of plants, animals, and humans, and in broad ecosystem functions. Thus, having an efficient species-level identification system could significantly enhance our ability to treat fungal diseases and to monitor the spatial and temporal patterns of fungal distributions and migrations. DNA barcoding is a potent approach for rapid identification of fungal specimens, generating novel species hypothesis, and guiding biodiversity and ecological studies. In this mini-review, I briefly summarize (i) the history of DNA sequence-based fungal identification; (ii) the emergence of the ITS region as the consensus primary fungal barcode; (iii) the use of the ITS barcodes to address a variety of issues on fungal diversity from local to global scales, including generating a large number of species hypothesis; and (iv) the problems with the ITS barcode region and the approaches to overcome these problems. Similar to DNA barcoding research on plants and animals, significant progress has been achieved over the last few years in terms of both the questions being addressed and the foundations being laid for future research endeavors. However, significant challenges remain. I suggest three broad areas of research to enhance the usefulness of fungal DNA barcoding to meet the current and future challenges: (i) develop a common set of primers and technologies that allow the amplification and sequencing of all fungi at both the primary and secondary barcode loci; (ii) compile a centralized reference database that includes all recognized fungal species as well as species hypothesis, and allows regular updates from the research community; and (iii) establish a consensus set of new species recognition criteria based on barcode DNA sequences that can be applied across the fungal kingdom.Key words: ITS, secondary barcode, herbarium, metabarcoding, operational taxonomic unit. Résumé :Les champignons sont présents partout, tant dans les environnements naturels qu'anthropisés. Ils jouent des rôles importants dans la santé des plantes, des animaux et des humains de même que dans les écosystèmes. Ainsi, la disponibilité d'un système efficace d'identification des espèces pourrait grandement augmenter la capacité de traiter les maladies fongiques et de surveiller les variations spatiales et temporelles dans la distribution et la migration des champignons. Le codage à barres de l'ADN est une approche potentiellement puissante pour l'identification rapide de spécimens fongiques, permettant d'identifier de nouvelles espèces et guidant les études sur la biodiversité et les écosystèmes. Dans cette mini-synthèse, l'auteur résume brièvement (i) l'histoire de l'identification des champignons sur la base de séquences d'ADN; (ii) l'émergence de la région ITS en tant que code à barre fongique primaire consensuel; (iii) l'emploi des codes à barres ITS pour étudier nombre de questions sur la diversité des champignons de l'échelle locale à globale, inc...

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“…However, the extracts of T. versicolor mushroom have been reported to be non-toxic to several normal cells [19][20][21] and in cancer patients on clinical trials [22][23][24]. Differences in the ecological zones where mushroom exist and the influence of some environmental factors may account for the overall composition and activity of compounds present in mushrooms [25,26]. This study therefore investigated the antiproliferative potential plates contained 100 µl RPMI-1640 with no cells as they were treated as blanks for each cell line.…”

Section: Introductionmentioning

confidence: 99%