THE IMPACT OF TALL-GRASS PRAIRIE RESTORATION ON SOIL COMPOSITION AND MICROBIAL COMMUNITIES, SEBASTIAN COUNTY, ARKANSAS

2019 ◽  
Author(s):  
Micah F. Weaver ◽  
◽  
Dave P. Mayo ◽  
Jeff Shaver ◽  
Jay Randolph
Keyword(s):  
Microbial Communities ◽  
Prairie Restoration ◽  
Soil Composition ◽  
Tall Grass ◽  
Tall Grass Prairie ◽  
The Impact

scholarly journals Population connectivity in voles (Microtus sp.) as a gauge for tall grass prairie restoration in midwestern North America

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0260344
Author(s):  
Marlis R. Douglas ◽  
Steven M. Mussmann ◽  
Tyler K. Chafin ◽  
Whitney J. B. Anthonysamy ◽  
Mark A. Davis ◽  
...  
Keyword(s):  
Genetic Structure ◽  
North America ◽  
Agricultural Land ◽  
Population Connectivity ◽  
Meadow Vole ◽  
Prairie Restoration ◽  
Tall Grass ◽  
Tall Grass Prairie ◽  
Agricultural Matrix ◽  
High Dispersal

Ecological restoration can promote biodiversity conservation in anthropogenically fragmented habitats, but effectiveness of these management efforts need to be statistically validated to determine ’success.’ One such approach is to gauge the extent of recolonization as a measure of landscape permeability and, in turn, population connectivity. In this context, we estimated dispersal and population connectivity in prairie vole (Microtus ochrogaster; N = 231) and meadow vole (M. pennsylvanicus; N = 83) within five tall-grass prairie restoration sites embedded within the agricultural matrix of midwestern North America. We predicted that vole dispersal would be constrained by the extent of agricultural land surrounding restored habitat patches, spatially isolating vole populations and resulting in significant genetic structure. We first employed genetic assignment tests based on 15 microsatellite DNA loci to validate field-derived species-designations, then tested reclassified samples with multivariate and Bayesian clustering to assay for spatial and temporal genetic structure. Population connectivity was further evaluated by calculating pairwise FST, then potential demographic effects explored by computing migration rates, effective population size (Ne), and average relatedness (r). Genetic species assignments reclassified 25% of initial field identifications (N = 11 M. ochrogaster; N = 67 M. pennsylvanicus). In M. ochrogaster population connectivity was high across the study area, reflected in little to no spatial or temporal genetic structure. In M. pennsylvanicus genetic structure was detected, but relatedness estimates identified it as kin-clustering instead, underscoring social behavior among populations rather than spatial isolation as the cause. Estimates of Ne and r were stable across years, reflecting high dispersal and demographic resilience. Combined, these metrics suggest the agricultural matrix is highly permeable for voles and does not impede dispersal. High connectivity observed confirms that the restored landscape is productive and permeable for specific management targets such as voles and also demonstrates population genetic assays as a tool to statistically evaluate effectiveness of conservation initiatives.

scholarly journals From the Ground Up: Prairies on Reclaimed Mine Land—Impacts on Soil and Vegetation

Land ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 455
Author(s):  
Rebecca M. Swab ◽  
Nicola Lorenz ◽  
Nathan R. Lee ◽  
Steven W. Culman ◽  
Richard P. Dick
Keyword(s):  
Organic Carbon ◽  
Soil Organic Carbon ◽  
Soil Properties ◽  
Plant Community ◽  
Prairie Restoration ◽  
Native Plant ◽  
Soil Microbial ◽  
Prairie Restorations ◽  
Mine Lands ◽  
The Impact

After strip mining, soils typically suffer from compaction, low nutrient availability, loss of soil organic carbon, and a compromised soil microbial community. Prairie restorations can improve ecosystem services on former agricultural lands, but prairie restorations on mine lands are relatively under-studied. This study investigated the impact of prairie restoration on mine lands, focusing on the plant community and soil properties. In southeast Ohio, 305 ha within a ~2000 ha area of former mine land was converted to native prairie through herbicide and planting between 1999–2016. Soil and vegetation sampling occurred from 2016–2018. Plant community composition shifted with prairie age, with highest native cover in the oldest prairie areas. Prairie plants were more abundant in older prairies. The oldest prairies had significantly more soil fungal biomass and higher soil microbial biomass. However, many soil properties (e.g., soil nutrients, β-glucosoidase activity, and soil organic carbon), as well as plant species diversity and richness trended higher in prairies, but were not significantly different from baseline cool-season grasslands. Overall, restoration with prairie plant communities slowly shifted soil properties, but mining disturbance was still the most significant driver in controlling soil properties. Prairie restoration on reclaimed mine land was effective in establishing a native plant community, with the associated ecosystem benefits.

scholarly journals Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Verónica Lloréns-Rico ◽  
Sara Vieira-Silva ◽  
Pedro J. Gonçalves ◽  
Gwen Falony ◽  
Jeroen Raes
Keyword(s):  
Microbial Communities ◽  
Quantitative Methods ◽  
Microbial Load ◽  
Metagenomic Sequencing ◽  
Sampling Depth ◽  
Microbiome Research ◽  
Microbiome Data ◽  
The Impact ◽  
Analytical Approaches ◽  
Quantitative Approaches

AbstractWhile metagenomic sequencing has become the tool of preference to study host-associated microbial communities, downstream analyses and clinical interpretation of microbiome data remains challenging due to the sparsity and compositionality of sequence matrices. Here, we evaluate both computational and experimental approaches proposed to mitigate the impact of these outstanding issues. Generating fecal metagenomes drawn from simulated microbial communities, we benchmark the performance of thirteen commonly used analytical approaches in terms of diversity estimation, identification of taxon-taxon associations, and assessment of taxon-metadata correlations under the challenge of varying microbial ecosystem loads. We find quantitative approaches including experimental procedures to incorporate microbial load variation in downstream analyses to perform significantly better than computational strategies designed to mitigate data compositionality and sparsity, not only improving the identification of true positive associations, but also reducing false positive detection. When analyzing simulated scenarios of low microbial load dysbiosis as observed in inflammatory pathologies, quantitative methods correcting for sampling depth show higher precision compared to uncorrected scaling. Overall, our findings advocate for a wider adoption of experimental quantitative approaches in microbiome research, yet also suggest preferred transformations for specific cases where determination of microbial load of samples is not feasible.

scholarly journals Microbial drivers of methane emissions from unrestored industrial salt ponds

2021 ◽  
Author(s):  
Jinglie Zhou ◽  
Susanna M. Theroux ◽  
Clifton P. Bueno de Mesquita ◽  
Wyatt H. Hartman ◽  
Ye Tian ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Methane Flux ◽  
Methane Emissions ◽  
Metagenomic Data ◽  
Rrna Gene ◽  
Salt Ponds ◽  
Salt Pond ◽  
Reference Wetlands ◽  
Reference Wetland ◽  
The Impact

AbstractWetlands are important carbon (C) sinks, yet many have been destroyed and converted to other uses over the past few centuries, including industrial salt making. A renewed focus on wetland ecosystem services (e.g., flood control, and habitat) has resulted in numerous restoration efforts whose effect on microbial communities is largely unexplored. We investigated the impact of restoration on microbial community composition, metabolic functional potential, and methane flux by analyzing sediment cores from two unrestored former industrial salt ponds, a restored former industrial salt pond, and a reference wetland. We observed elevated methane emissions from unrestored salt ponds compared to the restored and reference wetlands, which was positively correlated with salinity and sulfate across all samples. 16S rRNA gene amplicon and shotgun metagenomic data revealed that the restored salt pond harbored communities more phylogenetically and functionally similar to the reference wetland than to unrestored ponds. Archaeal methanogenesis genes were positively correlated with methane flux, as were genes encoding enzymes for bacterial methylphosphonate degradation, suggesting methane is generated both from bacterial methylphosphonate degradation and archaeal methanogenesis in these sites. These observations demonstrate that restoration effectively converted industrial salt pond microbial communities back to compositions more similar to reference wetlands and lowered salinities, sulfate concentrations, and methane emissions.

The impact of nanoscale zero-valent iron particles on soil microbial communities is soil dependent

2019 ◽  
Vol 364 ◽  
pp. 591-599 ◽  
Author(s):  
María T. Gómez-Sagasti ◽  
Lur Epelde ◽  
Mikel Anza ◽  
Julen Urra ◽  
Itziar Alkorta ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Zero Valent Iron ◽  
Iron Particles ◽  
Soil Microbial ◽  
Nanoscale Zero Valent Iron ◽  
The Impact

scholarly journals Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise

2017 ◽  
Author(s):  
Taha Soliman ◽  
Sung-Yin Yang ◽  
Tomoko Yamazaki ◽  
Holger Jenke-Kodama
Keyword(s):  
Next Generation Sequencing ◽  
Microbial Communities ◽  
Dna Extraction ◽  
Dna Isolation ◽  
Soil Microbial Communities ◽  
Next Generation ◽  
Microbial Composition ◽  
Okinawa Island ◽  
The Impact ◽  
Generation Sequencing

Structure and diversity of microbial communities are an important research topic in biology, since microbes play essential roles in the ecology of various environments. Different DNA isolation protocols can lead to data bias and can affect results of next-generation sequencing. To evaluate the impact of protocols for DNA isolation from soil samples and also the influence of individual handling of samples, we compared results obtained by two researchers (R and T) using two different DNA extraction kits: (1) MO BIO PowerSoil® DNA Isolation kit (MO_R and MO_T) and (2) NucleoSpin® Soil kit (MN_R and MN_T). Samples were collected from six different sites on Okinawa Island, Japan. For all sites, differences in the results of microbial composition analyses (bacteria, archaea, fungi, and other eukaryotes), obtained by the two researchers using the two kits, were analyzed. For both researchers, the MN kit gave significantly higher yields of genomic DNA at all sites compared to the MO kit (ANOVA; P <0.006). In addition, operational taxonomic units for some phyla and classes were missed in some cases: Micrarchaea were detected only in the MN_T and MO_R analyses; the bacterial phylum Armatimonadetes was detected only in MO_R and MO_T; and WIM5 of the phylum Amoebozoa of eukaryotes was found only in the MO_T analysis. Our results suggest the possibility of handling bias; therefore, it is crucial that replicated DNA extraction be performed by at least two technicians for thorough microbial analyses and to obtain accurate estimates of microbial diversity.

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