The impact of host rock geochemistry on bacterial community structure in oligotrophic cave environments

Barton, Hazel A.; Taylor, Nicholas M.; Kreate, Michael P.; Springer, Austin C.; Oehrle, Stuart A.; Bertog, Janet L.

doi:10.5038/1827-806x.36.2.5

Cited by 108 publications

(70 citation statements)

References 44 publications

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“…However, rocks and minerals can be viewed as nutritive reserves and biogeochemical interfaces (24,25), where biotic mineral weathering represents a key process in nutrient cycling. Mineral colonization by macro-and microorganisms has been largely reported in many terrestrial and aquatic environments, where minerals are directly accessible and in contact with air or water (4,(26)(27)(28)(29). In contrast, few studies have investigated bacterial communities that colonize soil minerals and their role in nutrient cycling (30)(31)(32)(33)(34).…”

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confidence: 99%

Mineral Types and Tree Species Determine the Functional and Taxonomic Structures of Forest Soil Bacterial Communities

Colin

Nicolitch

Turpault³

et al. 2017

Appl Environ Microbiol

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Although minerals represent important soil constituents, their impact on the diversity and structure of soil microbial communities remains poorly documented. In this study, pure mineral particles with various chemistries (i.e., obsidian, apatite, and calcite) were considered. Each mineral type was conditioned in mesh bags and incubated in soil below different tree stands (beech, coppice with standards, and Corsican pine) for 2.5 years to determine the relative impacts of mineralogy and mineral weatherability on the taxonomic and functional diversities of mineral-associated bacterial communities. After this incubation period, the minerals and the surrounding bulk soil were collected to determine mass loss and to perform soil analyses, enzymatic assays, and cultivation-dependent and -independent analyses. Notably, our 16S rRNA gene pyrosequencing analyses revealed that after the 2.5-year incubation period, the mineral-associated bacterial communities strongly differed from those of the surrounding bulk soil for all tree stands considered. When focusing only on minerals, our analyses showed that the bacterial communities associated with calcite, the less recalcitrant mineral type, significantly differed from those that colonized obsidian and apatite minerals. The cultivation-dependent analysis revealed significantly higher abundances of effective mineral-weathering bacteria on the most recalcitrant minerals (i.e., apatite and obsidian). Together, our data showed an enrichment of Betaproteobacteria and effective mineral-weathering bacteria related to the Burkholderia and Collimonas genera on the minerals, suggesting a key role for these taxa in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems.IMPORTANCE Forests are usually developed on nutrient-poor and rocky soils, while nutrient-rich soils have been dedicated to agriculture. In this context, nutrient recycling and nutrient access are key processes in such environments. Deciphering how soil mineralogy influences the diversity, structure, and function of soil bacterial communities in relation to the soil conditions is crucial to better understanding the relative role of the soil bacterial communities in nutrient cycling and plant nutrition in nutrient-poor environments. The present study determined in detail the diversity and structure of bacterial communities associated with different mineral types incubated for 2.5 years in the soil under different tree species using cultivationdependent and -independent analyses. Our data showed an enrichment of specific bacterial taxa on the minerals, specifically on the most weathered minerals, suggesting that they play key roles in mineral weathering and nutrient cycling in nutrientpoor forest ecosystems.KEYWORDS mineral chemistry, bacterial communities, forest soil, mesh bags, mineral weatherability

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Mineral Types and Tree Species Determine the Functional and Taxonomic Structures of Forest Soil Bacterial Communities

Colin

Nicolitch

Turpault³

et al. 2017

Appl Environ Microbiol

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“…Such organic acids may then permit the growth of additional microbial species, which can use them as a source of carbon and energy (46)(47)(48)51). The production of these organic acids may therefore promote resource sharing and allow the establishment of morecomplex microbial communities, similar to those we have identified in extremely starved cave environments (Ͻ0.5 mg/liter total organic carbon) (10,11). If these organic acids are available for microbial growth, then it should be possible to detect the presence of these compounds within the environment.…”

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confidence: 62%

“…This research has been geared toward understanding what carbon and energy sources drive microbial community subsistence and growth during extreme starvation, allowing us to identify the ecological mechanisms that drive high species diversity in cave environments (7). Past work suggests that soil-derived humic and fulvic acids can percolate significant distances (Ͼ300 m) into the subsurface and provide a source of nutrients and energy (10,11). It is our hypothesis that these aromatic and polyaromatic soil-derived compounds contribute to the overall energy budget of these systems.…”

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confidence: 99%

“…Nonetheless, such high levels of biomass are not normally associated with surfaces under nutrient-limited conditions, suggesting that such accumulation may be less of an issue for environmental measurements (8,11,12). The preliminary work testing ATR-FTIR spectroscopy as an analytical tool for metabolic products under these conditions was carried out on pure calcite (Ͼ99% CaCO 3 ) crystals using relatively high concentrations of organic acid; however, these results did not demonstrate that such a technique would work under the complex geochemical conditions and low metabolic activity normally associated with cave samples (8,11,37). We therefore tested the ability of this technique to analyze microbial metabolic activity on calcite crystals and a limestone slide that were placed in a low-nutrient cave environment.…”

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confidence: 99%

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Use of Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy To Identify Microbial Metabolic Products on Carbonate Mineral Surfaces

Bullen¹,

Oehrle²,

Bennett

et al. 2008

Appl Environ Microbiol

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This paper demonstrates the use of attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy to detect microbial metabolic products on carbonate mineral surfaces. By creating an ATR-FTIR spectral database for specific organic acids using ATR-FTIR spectroscopy we were able to distinguish metabolic acids on calcite surfaces following Escherichia coli growth. The production of these acids by E. coli was verified using high-performance liquid chromatography with refractive index detection. The development of this technique has allowed us to identify microbial metabolic products on carbonate surfaces in nutrientlimited cave environments.Molecular phylogenetic analysis using the 16S rRNA gene sequence has revolutionized microbiology, allowing investigators to create comparative and evolutionary phylogenies for microbial species (49, 50). Phylogenetic placement also allows metabolic inference for the activity of previously uncultivated species within the environment, dramatically changing our understanding of microbial ecology and the role of microbial species within the biosphere (3, 36, 41). While metabolic inference is a valuable tool for estimating metabolic activity, specific metabolic responses to environmental conditions are harder to estimate, even for closely related species (1,24). To overcome such limitations, investigators can employ a number of different techniques to relate identified microbial phylotypes to environmental metabolic activities, including the use of isotopic probing and quantitative mRNA and metagenomic analyses (43).

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“…They are also released into an air forming bioaerosol containing 68 to 113 cfu m -3 of a cave air [44]. Molecular tools have reported that the major group of bacteria in a subterranean habitat is represented by Proteobacteria; however, the majority of isolates are strains of Actinobacteria [45].…”

Section: Introductionmentioning

confidence: 99%

Assessment of Airborne Actinomycetes in Subterranean and Earth Sanatoriums / Występowanie Promieniowców W Pomieszczeniu Sanatoriów Podziemnym Oraz Naziemnym

Frączek¹,

Kozdrój²

2013

Ecological Chemistry and Engineering S

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Actinomycetes are common soil microorganisms; however, they have also been detected in air samples, becoming important air contaminants in occupational and residential habitats. Concentrations of airborne actinomycetes and their distribution among different fractions of bioaerosol were determined in selected sites of two sanatorium types, ie a subterranean located in the former salt-mine of Bochnia and standard earth spa of Szczawnica. The average concentrations of actinomycetes ranged from 0 to almost 40 cfu m -3, for the sanatorium of Bochnia, and from 7 to 125 cfu m -3 , for Szczawnica spa, throughout the year. The respiratory fraction of the bioaerosol ranged from 25 to 51% and from 78 to 81% in the subterranean sites and rooms of Szczawnica spa, respectively. For both sanatoriums, among isolated actinomycetes dominated species belonging to Rhodococcus, Streptomyces and Nocardia. The results indicate that patients can be differentially exposed to airborne actinomycetes in compared sanatoriums. The air of underground spa reveals to be of better quality, regarding the bacteria characteristics.

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The impact of host rock geochemistry on bacterial community structure in oligotrophic cave environments

Cited by 108 publications

References 44 publications

Mineral Types and Tree Species Determine the Functional and Taxonomic Structures of Forest Soil Bacterial Communities

Mineral Types and Tree Species Determine the Functional and Taxonomic Structures of Forest Soil Bacterial Communities

Use of Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy To Identify Microbial Metabolic Products on Carbonate Mineral Surfaces

Assessment of Airborne Actinomycetes in Subterranean and Earth Sanatoriums / Występowanie Promieniowców W Pomieszczeniu Sanatoriów Podziemnym Oraz Naziemnym

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