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Culture-independent analysis of the soil bacterial assemblage at the Great Salt Plains of Oklahoma.

ABSTRACT: The Great Salt Plains (GSP) of Oklahoma is a natural inland terrestrial hypersaline environment that forms evaporite crusts of mainly NaCl. Previous work described GSP bacterial assemblages through the phylogenetic and phenetic characterization of 105 isolates from 46 phylotypes. The current report describes the same bacterial assemblages through culture-independent 16S rRNA gene clone libraries. Although from similar hypersaline mud flats, the bacterial libraries from two sites, WP3 and WP6, were quite different. The WP3 library was dominated by cyanobacteria, mainly Cyanothece and Euhalothece. The WP6 library was rich in anaerobic sulfur-cycle organisms, including abundant Desulfuromonas. This pattern likely reflects differences in abiotic factors, such as frequency of flooding and hydrologic push. While more than 100 OTUs were identified, the assemblages were not as diverse, based on Shannon indexes, as bacterial communities from oligohaline soils. Since natural inland hypersaline soils are relatively unstudied, it was not clear what kind of bacteria would be present. The bacterial assemblage is predominantly genera typically found in hypersaline systems, although some were relatives of microbes common in oligohaline and marine environments. The bacterial clones did not reflect wide functional diversity, beyond phototrophs, sulfur metabolizers, and numerous heterotrophs.

SUBMITTER: Caton IR

PROVIDER: S-EPMC3597346 | biostudies-literature | 2012 Feb

REPOSITORIES: biostudies-literature

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Culture-independent analysis of the soil bacterial assemblage at the Great Salt Plains of Oklahoma.

Caton Ingrid R IR Schneegurt Mark A MA

Journal of basic microbiology 20110923 1

The Great Salt Plains (GSP) of Oklahoma is a natural inland terrestrial hypersaline environment that forms evaporite crusts of mainly NaCl. Previous work described GSP bacterial assemblages through the phylogenetic and phenetic characterization of 105 isolates from 46 phylotypes. The current report describes the same bacterial assemblages through culture-independent 16S rRNA gene clone libraries. Although from similar hypersaline mud flats, the bacterial libraries from two sites, WP3 and WP6, we ...[more]

PMID: 21953014

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Project description:Decomposing vertebrates impact ecosystems by stimulating animal, insect, and microbial scavengers, perturbing biogeochemical cycles, and transferring elements back to the environment. Most studies exploring the impacts of vertebrate decomposition focus on surface decay scenarios over timescales of days to years. Accordingly, our knowledge of ecosystem impacts of vertebrate decomposition in burial contexts and over longer time scales is limited. In 2000, six animal carcasses were buried in a shallow grave (<1.0 m) and allowed to decompose naturally until partial excavation in 2021, enabling evaluation of long-term soil biogeochemical responses to decomposing vertebrates. Soils were sampled along three vertical transects from the surface to the bone-bearing layer (~40 cm depth) and below. Comparison of the physical and chemical properties of the grave and control soils from equivalent depths indicate significant perturbations even 21 years after burial. Notably, soil pH was significantly more acidic in grave soils (p = 0.0296), and conductivity was significantly elevated (p = 0.0009). Grave soils were significantly enriched with respect to nitrogen stable isotopes, exhibiting δ15N values of 10.48 ± 3.6‰, which is ~5‰ greater than controls. Carbon and nitrogen content was also disrupted in the burial, with five times more nitrogen in the bone-bearing layer and almost double the carbon. Water and acid-based extractions of soils revealed significant differences between grave and control soils, driven largely by calcium, phosphorus (P), magnesium, and iron concentrations. P concentrations in acid extracts were significantly enriched at the bone-bearing layer, suggesting release of P from the bones. This study demonstrates that decomposition may result in long-lived impacts to burial environments and soil biogeochemistry, even after soft tissues decay. While not typically considered in ecosystem models, buried remains contribute to soils for decades or longer, and soil biogeochemistry serves a critical role in facilitating or preventing the long-term preservation of bone.

Project description:Although a number of different methods have been used to quantify soil bacteria, identifying the optimal method(s) for soil bacterial abundance is still in question. No single method exists for undertaking an absolute microbial count using culture-dependent methods (CDMs) or even culture-independent methods (CIMs). This study investigated soil storage and pretreatment methods for optimal bacterial counts. Appropriate storage temperature (4°C) and optimal pretreatment methods (sonication time for 3 min and centrifugation at 1400 g) were necessary to preserve bacterial cell viability and eliminate interference from soil particles. To better estimate soil bacterial numbers under various cellular state and respiration, this study also evaluated three CDMs (i.e., colony forming unit, spotting, and most probable number (MPN) and three CIMs (i.e., flow cytometry (FCM), epifluorescence microscopy (EM) count, and DNA quantitation). Each counting method was tested using 72 soil samples collected from a local arable farm site at three different depths (i.e., 10-20, 90-100, and 180-190 cm). Among all CDMs, MPN was found to be rapid, simple, and reliable. However, the number of bacteria quantified by MPN was 1-2 orders lower than that quantified by CIMs, likely due to the inability of MPN to count anaerobic bacteria. The DNA quantitation method appeared to overestimate soil bacterial numbers, which may be attributed to DNA from dead bacteria and free DNA in the soil matrix. FCM was found to be ineffective in counting soil bacteria as it was difficult to separate the bacterial cells from the soil particles. Dyes used in FCM stained the bacterial DNA and clay particles. The EM count was deemed a highly effective method as it provided information on soil mineral particles, live bacteria, and dead bacteria; however, it was a time-consuming and labor-intensive process. Combining both types of methods was considered the best approach to acquire better information on the characteristics of indigenous soil microorganisms (aerobic versus anaerobic, live versus dead).

Dataset Information

Culture-independent analysis of the soil bacterial assemblage at the Great Salt Plains of Oklahoma.

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Culture-independent analysis of the soil bacterial assemblage at the Great Salt Plains of Oklahoma.

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