Bacterial diversity differences along an epigenic cave stream reveal evidence of community dynamics, succession, and stability

Brannen-Donnelly, Kathleen Merritt; Engel, Annette Summers

doi:10.3389/fmicb.2015.00729

Cited by 20 publications

(18 citation statements)

References 60 publications

(104 reference statements)

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“…However, we did find significant differences among bacterial communities in terms of their occupied niches (i.e., air, rock, sediment, and water), not unlike Brannen-Donnelly and Engel (2015) who reported that bacterial community composition in cave streams and sediments differed at the class level. More recently, Alonso et al (2018) reported that mineral substrate was the most significant factor determining cave microbial diversity and structure.…”

Section: Discussioncontrasting

confidence: 99%

Diversity, Distribution and Co-occurrence Patterns of Bacterial Communities in a Karst Cave System

et al. 2019

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Caves are typified by their permanent darkness and a shortage of nutrients. Consequently, bacteria play an important role in sustaining such subsurface ecosystems by dominating primary production and fueling biogeochemical cycles. China has one of the world’s largest areas of karst topography in the Yunnan-Guizhou Plateau, yet the bacteriomes in these karst caves remain unexplored. In this study, bacteriomes of eight karst caves in southwest China were examined, and co-occurrence networks of cave bacterial communities were constructed. Results revealed abundant and diversified bacterial communities in karst caves, with Proteobacteria , Actinobacteria , and Firmicutes being the most abundant phyla. Statistical analysis revealed no significant difference in bacteriomes among the eight caves. However, a PCoA plot did show that the bacterial communities of 128 cave samples clustered into groups corresponding to sampling types (air, water, rock, and sediment). These results suggest that the distribution of bacterial communities is driven more by sample types than the separate caves from which samples were collected. Further community-level composition analysis indicated that Proteobacteria were most dominant in water and air samples, while Actinobacteria dominated the sediment and rock samples. Co-occurrence analysis revealed highly modularized assembly patterns of the cave bacterial community, with Nitrosococcaceae wb1-P19, an uncultured group in Rokubacteriales , and an uncultured group in Gaiellales , being the top-three keystone members. These results not only expand our understanding of cave bacteriomes but also inspires functional exploration of bacterial strains in karst caves.

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Section: Discussioncontrasting

confidence: 99%

Diversity, Distribution and Co-occurrence Patterns of Bacterial Communities in a Karst Cave System

et al. 2019

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“…These sites were chosen based on oligotrophic conditions, sampling of pelagic microbial communities, and 454-pyrosequencing. These comparative samples included: the Edwards karst aquifer of Texas (Edwards aquifer; SRP010407; Engel and Randall, 2011 ); a shallow karst aquifer in Germany (Limestone aquifer; ERP020663; Herrmann et al, 2017 ); stream water in a Kentucky epigenic cave (Cascade Cave system; SRP058014; Brannen-Donnelly and Engel, 2015 ); and a surface lake open to photosynthetic input (the oligotrophic Lake Brienz; SRP021556; Köllner et al, 2013 ; Figure 5A ). Analyses are therefore based on sequencing method (454-pyrosequencing), PCR primers and average number of amplicons.…”

Section: Resultsmentioning

confidence: 99%

High Microbial Diversity Despite Extremely Low Biomass in a Deep Karst Aquifer

et al. 2018

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Despite the importance of karst aquifers as a source of drinking water, little is known about the role of microorganisms in maintaining the quality of this water. One of the limitations in exploring the microbiology of these environments is access, which is usually limited to wells and surface springs. In this study, we compared the microbiology of the Madison karst aquifer sampled via the potentiometric lakes of Wind Cave with surface sampling wells and a spring. Our data indicated that only the Streeter Well (STR), which is drilled into the same hydrogeologic domain as the Wind Cave Lakes (WCL), allowed access to water with the same low biomass (1.56–9.25 × 103 cells mL-1). Filtration of ∼300 L of water from both of these sites through a 0.2 μm filter allowed the collection of sufficient cells for DNA extraction, PCR amplification of 16S rRNA gene sequences, and identification through pyrosequencing. The results indicated that bacteria (with limited archaea and no detectable eukaryotic organisms) dominated both water samples; however, there were significant taxonomic differences in the bacterial populations of the samples. The STR sample was dominated by a single phylotype within the Gammaproteobacteria (Order Acidithiobacillales), which dramatically reduced the overall diversity and species richness of the population. In WCL, despite less organic carbon, the bacterial population was significantly more diverse, including significant contributions from the Gammaproteobacteria, Firmicutes, Chloroflexi, Actinobacteria, Planctomycetes, Fusobacter, and Omnitrophica phyla. Comparisons with similar oligotrophic environments suggest that karst aquifers have a greater species richness than comparable surface environs. These data also demonstrate that Wind Cave provides a unique opportunity to sample a deep, subterranean aquifer directly, and that the microbiology of such aquifers may be more complex than previously anticipated.

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“…Additionally, the first indications of organic structures became visible (e.g., 12 months). The scale bars indicate the extent of magnification investigations of stagnant cave pools in the epiphreatic zone of a karst system (Shabarova et al, 2013(Shabarova et al, , 2014Shabarova & Pernthaler, 2010) and an epigenic cave stream (Brannen-Donnelly & Engel, 2015) indeed indicated the presence of stable and transient bacterial populations. For example, Shabarova et al (2014) defined a bacterial "core" assemblage as the subset of those bacterial genotypes that were present in all samples during their temporal study of the bacterial community development in stagnant rock pools.…”

Section: Defining the Amec Versus Tmec Conceptmentioning

confidence: 99%

“…The aim of this concept is to predict the proportion of AMEC versus TMEC and its typical range of variation in spring water according to the catchment and the hydrogeology of the investigated system. To facilitate its correct understanding and interpretation (Brannen‐Donnelly & Engel, ; Wilhartitz & Farnleitner, ), the concept is described in more detail in the following section. Microbes that are unable to proliferate and unable to form stable populations within the karst aquifer are considered TMEC.…”

Section: Occurrence Of Microbial Communities In Spring Water Of Alpinmentioning

confidence: 99%

Opening the black box of spring water microbiology from alpine karst aquifers to support proactive drinking water resource management

et al. 2018

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Over the past 15 years, pioneering interdisciplinary research has been performed on the microbiology of hydrogeologically well‐defined alpine karst springs located in the Northern Calcareous Alps (NCA) of Austria. This article gives an overview on these activities and links them to other relevant research. Results from the NCA springs and comparable sites revealed that spring water harbors abundant natural microbial communities even in aquifers with high water residence times and the absence of immediate surface influence. Apparently, hydrogeology has a strong impact on the concentration and size of the observed microbes, and total cell counts (TCC) were suggested as a useful means for spring type classification. Measurement of microbial activities at the NCA springs revealed extremely low microbial growth rates in the base flow component of the studied spring waters and indicated the importance of biofilm‐associated microbial activities in sediments and on rock surfaces. Based on genetic analysis, the autochthonous microbial endokarst community (AMEC) versus transient microbial endokarst community (TMEC) concept was proposed for the NCA springs, and further details within this overview article are given to prompt its future evaluation. In this regard, it is well known that during high‐discharge situations, surface‐associated microbes and nutrients such as from soil habitats or human settlements—potentially containing fecal‐associated pathogens as the most critical water‐quality hazard—may be rapidly flushed into vulnerable karst aquifers. In this context, a framework for the comprehensive analysis of microbial pollution has been proposed for the NCA springs to support the sustainable management of drinking water safety in accordance with recent World Health Organization guidelines. Near‐real‐time online water quality monitoring, microbial source tracking (MST) and MST‐guided quantitative microbial‐risk assessment (QMRA) are examples of the proposed analytical tools. In this context, this overview article also provides a short introduction to recently emerging methodologies in microbiological diagnostics to support reading for the practitioner. Finally, the article highlights future research and development needs.This article is categorized under: Engineering Water > Water, Health, and SanitationScience of Water > Water ExtremesWater and Life > Nature of Freshwater Ecosystems

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Bacterial diversity differences along an epigenic cave stream reveal evidence of community dynamics, succession, and stability

Cited by 20 publications

References 60 publications

Diversity, Distribution and Co-occurrence Patterns of Bacterial Communities in a Karst Cave System

Diversity, Distribution and Co-occurrence Patterns of Bacterial Communities in a Karst Cave System

High Microbial Diversity Despite Extremely Low Biomass in a Deep Karst Aquifer

Opening the black box of spring water microbiology from alpine karst aquifers to support proactive drinking water resource management

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