GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity

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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...

Section: Methodsmentioning

confidence: 99%

Distance-Decay Relationship for Biological Wastewater Treatment Plants

Wang

Wen

Deng

et al. 2016

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“…The community DNA was extracted using a freeze-grinding method (24) and quantified with PicoGreen (25) (Quant-It PicoGreen kit; Invitrogen, Carlsbad, CA). DNA (20 ng) was amplified using whole-community genome amplification with a TempliPhi kit (GE Healthcare, Piscataway, NJ), and 3.0 g amplified DNA was hybridized to the GeoChip 3.0 as previously described (26,27). The hybridized GeoChip was scanned, and the signal intensity for each spot was determined using ImaGene 6.0 (Biodiscovery, El Segundo, CA).…”

Section: Methodsmentioning

confidence: 99%

Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction

Zhang

Nostrand

et al. 2015

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A pilot-scale field experiment demonstrated that a one-time amendment of emulsified vegetable oil (EVO) reduced groundwater U(VI) concentrations for 1 year in a fast-flowing aquifer. However, little is known about how EVO amendment stimulates the functional gene composition, structure, and dynamics of groundwater microbial communities toward prolonged U(VI) reduction. In this study, we hypothesized that EVO amendment would shift the functional gene composition and structure of groundwater microbial communities and stimulate key functional genes/groups involved in EVO biodegradation and reduction of electron acceptors in the aquifer. To test these hypotheses, groundwater microbial communities after EVO amendment were analyzed using a comprehensive functional gene microarray. Our results showed that EVO amendment stimulated sequential shifts in the functional composition and structure of groundwater microbial communities. Particularly, the relative abundance of key functional genes/groups involved in EVO biodegradation and the reduction of NO 3 ؊ , Mn(IV), Fe(III), U(VI), and SO 4 2؊ significantly increased, especially during the active U(VI) reduction period. The relative abundance for some of these key functional genes/groups remained elevated over 9 months. Montel tests suggested that the dynamics in the abundance, composition, and structure of these key functional genes/groups were significantly correlated with groundwater concentrations of acetate, NO 3 ؊ , Mn(II), Fe(II), U(VI), and SO 4 2؊ . Our results suggest that EVO amendment stimulated dynamic succession of key functional microbial communities. This study improves our understanding of the composition, structure, and function changes needed for groundwater microbial communities to sustain a long-term U(VI) reduction. Mining, ore processing, and weapons and fuel production have left many sites around the world contaminated with uranium (U) (1). Groundwater contamination in particular is a critical public concern because the transport of highly soluble and toxic U(VI) within groundwater threatens drinking water resources. Bioreduction of U(VI) to insoluble U(IV) has been recognized as an effective approach to immobilize U in situ (2). However, while microorganisms capable of U(VI) reduction are present in aquifers, U(VI) still persists because of the lack of available electron donors and, in some cases, the presence of excess competing electron acceptors (e.g., NO 3 Ϫ ) (3). Injection of a substrate that would provide electron donors is essential to stimulate indigenous microbial communities toward U(VI) reduction (4, 5).Some U.S. Department of Energy (DOE) sites, for example, the Oak Ridge Integrated Field Research Challenge (ORIFRC) and the Old Rifle uranium mill tailing remedial action sites, are contaminated with U(VI). To remediate these sites, various fast-degrading substrates (e.g., acetate, ethanol, and lactate) have been used. The substrate injection stimulated microbial populations important to U(VI) reduction, resulting in distinct microbial co...

“…Both the 16S rRNA-based prediction and the GeoChip 5.0 analysis, which has been used to assess the metabolic pathways in other ecosystems (40,42,(61)(62)(63), showed that these communities possess a diverse and versatile metabolic potential. However, communities were separated based on plant microenvironment only via GeoChip analysis, indicating that predictions can yield valuable global information but may not be an adequate reflection of the community variations detected only when analyzing samples directly.…”

Section: Figmentioning

confidence: 99%

Microbial and Functional Diversity within the Phyllosphere of Espeletia Species in an Andean High-Mountain Ecosystem

Ruiz-Pérez

Restrepo

Zambrano

2016

c Microbial populations residing in close contact with plants can be found in the rhizosphere, in the phyllosphere as epiphytes on the surface, or inside plants as endophytes. Here, we analyzed the microbiota associated with Espeletia plants, endemic to the Páramo environment of the Andes Mountains and a unique model for studying microbial populations and their adaptations to the adverse conditions of high-mountain neotropical ecosystems. Communities were analyzed using samples from the rhizosphere, necromass, and young and mature leaves, the last two analyzed separately as endophytes and epiphytes. The taxonomic composition determined by performing sequencing of the V5-V6 region of the 16S rRNA gene indicated differences among populations of the leaf phyllosphere, the necromass, and the rhizosphere, with predominance of some phyla but only few shared operational taxonomic units (OTUs). Functional profiles predicted on the basis of taxonomic affiliations differed from those obtained by GeoChip microarray analysis, which separated community functional capacities based on plant microenvironment. The identified metabolic pathways provided insight regarding microbial strategies for colonization and survival in these ecosystems. This study of novel plant phyllosphere microbiomes and their putative functional ecology is also the first step for future bioprospecting studies in search of enzymes, compounds, or microorganisms relevant to industry or for remediation efforts.A ndean high-mountain environments have been reported as diversity hot spots, mainly because of their endemic species (1). The Paramos ecosystems within the Neotropical Andes consist of isolated, high-elevation areas that are reported to be the world's fastest-evolving biodiversity hot spot (2). These ecosystems are exposed to harsh environmental conditions, such as high incidence of UV radiation (3) and daily shifts in temperatures that impose selective pressure on native plants and their associated microbiota (4). In particular, the phyllosphere of endemic plants from Paramos represents a unique ecosystem for microbial communities with diverse and distinctive abilities to survive under conditions considered extreme for other forms of life.The phyllosphere refers to all aboveground surfaces of any plant, including leaves, stems, buds, flowers, and fruits (5). It acts as a landing stage where spores or other propagules can develop and multiply (6) and has been reported as probably the largest ecosystem on earth colonized by microorganisms, mainly bacteria and fungi (7). Interest in studying the phyllosphere microbiota is growing due to its potential in terms of microbial interactions, survival under harsh environmental, nutrient or humidity conditions, and bioprospecting. The most emblematic plant in the Colombian Paramos is known as "frailejón," a plant endemic to the region and belonging to the genus Espeletia (8, 9). These plants have unique adaptations that enable them to resist exposure to UV light and daily temperature changes; they are in close ...