Bushfire impacts on a threatened swamp ecosystem: responses of the soil microbial communities and restoration

2021 ◽  
Author(s):  
Nathali Machado de Lima ◽  
Alexandria Thomsen ◽  
Mark Ooi ◽  
Miriam Muñoz-Rojas
Keyword(s):  
Microbial Communities ◽  
Longwall Mining ◽  
Soil Microbial Communities ◽  
Environmental Indicators ◽  
Fire Season ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Drought Period ◽  
Soil Microbial ◽  
The Impact

<p>Australia faced the most extreme and prolonged fire season in 2019-2020, resulting in tragic habitat loss for many threatened species and the destruction of many ecological communities.  Newnes Plateau Shrub Swamps are peatlands located in the upper Blue Mountains region of New South Wales, Australia. These ecosystems perform many important ecological functions while absorbing and filtering water and releasing it slowly back to the environment. Their functions are related to the control of peak flow events, water purification and the harboring of many threatened plant and animal species. Despite their ecological importance, the area has been intensively degraded through longwall mining processes, resulting in the lowering and loss of water tables in the area. In December 2019 these impacts were compounded by an intense prolonged drought period and extensive wildfire. While the effects of these combined factors on the vegetation have been analysed and revealed remarkable negative impacts in the swamps under mining pressures, the effects on the soil microbial communities and related soil functions have not yet been studied. To investigate both drivers (fire and mining activities), we selected three mined swamps and three unmined swamps to assess their soil microbial composition and diversity through Next Generation Sequencing, and to characterise the soil chemical composition. At each site, we collected samples considering three treatments, one in the swamp valley fill and two at two different heights of the swamp valley margin, focusing on the soil close to specific groups of plants (e.g. sedges and shrubs). For each site and treatment, three soil samples (~ 10 m from each other) of 10x10 cm and ~ 3 to 5 cm of depth were collected using a trowel. We aim to build 16S rRNA gene libraries and co-relate them with the soil chemical variables, to assess the impact on these microbial communities and their possible use as environmental indicators and basis for future applied initiatives in conservation and restoration.</p><p> </p>

scholarly journals Hidden heterogeneity and co-occurrence networks of soil prokaryotic communities revealed at the scale of individual soil aggregates

2020 ◽  
Author(s):  
Márton Szoboszlay ◽  
Christoph C. Tebbe
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Spatial Information ◽  
Soil Aggregates ◽  
Soil Microbial Communities ◽  
Rrna Gene ◽  
Ammonium Oxidation ◽  
Soil Microbial ◽  
The Impact

AbstractSequencing PCR-amplified gene fragments from metagenomic DNA is a widely applied method for studying the diversity and dynamics of soil microbial communities. Typically DNA is extracted from 0.25 to 1 g of soil. These amounts, however, neglect the heterogeneity of soil present at the scale of soil aggregates; and thus, ignore a crucial scale for understanding the structure and functionality of soil microbial communities. Here we show with a nitrogen-depleted agricultural soil the impact of reducing the amount of soil used for DNA extraction from 250 mg to approx. 1 mg in order to access spatial information on the prokaryotic community structure as indicated by 16S rRNA-gene amplicon analyses. Furthermore, we demonstrate that individual aggregates from the same soil differ in their prokaryotic communities. The analysis of 16S rRNA gene amplicon sequences from individual soil aggregates allowed us, in contrast to 250 mg soil samples, to construct a co-occurrence network that provides insight into the structure of microbial associations in the studied soil. Two dense clusters were apparent in the network, one dominated by Thaumarchaeota, known to be capable of ammonium oxidation at low N concentrations, and the other by Acidobacteria subgroup 6 probably representing an oligotrophic lifestyle to obtain energy from SOC. Overall this study demonstrates that DNA obtained from individual soil aggregates provides new insights into how microbial communities are assembled.

scholarly journals Landscape Position Influences Microbial Composition and Function via Redistribution of Soil Water across a Watershed

2015 ◽  
Vol 81 (24) ◽  
pp. 8457-8468 ◽  
Author(s):  
Zhe Du ◽  
Diego A. Riveros-Iregui ◽  
Ryan T. Jones ◽  
Timothy R. McDermott ◽  
John E. Dore ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Water Content ◽  
Soil Water ◽  
Environmental Conditions ◽  
Soil Microbial Communities ◽  
Subalpine Forest ◽  
Rrna Gene ◽  
Type I ◽  
Microbial Composition ◽  
Soil Microbial

ABSTRACTSubalpine forest ecosystems influence global carbon cycling. However, little is known about the compositions of their soil microbial communities and how these may vary with soil environmental conditions. The goal of this study was to characterize the soil microbial communities in a subalpine forest watershed in central Montana (Stringer Creek Watershed within the Tenderfoot Creek Experimental Forest) and to investigate their relationships with environmental conditions and soil carbonaceous gases. As assessed by tagged Illumina sequencing of the 16S rRNA gene, community composition and structure differed significantly among three landscape positions: high upland zones (HUZ), low upland zones (LUZ), and riparian zones (RZ). Soil depth effects on phylogenetic diversity and β-diversity varied across landscape positions, being more evident in RZ than in HUZ. Mantel tests revealed significant correlations between microbial community assembly patterns and the soil environmental factors tested (water content, temperature, oxygen, and pH) and soil carbonaceous gases (carbon dioxide concentration and efflux and methane concentration). With one exception, methanogens were detected only in RZ soils. In contrast, methanotrophs were detected in all three landscape positions. Type I methanotrophs dominated RZ soils, while type II methanotrophs dominated LUZ and HUZ soils. The relative abundances of methanotroph populations correlated positively with soil water content (R= 0.72,P< 0.001) and negatively with soil oxygen (R= −0.53,P= 0.008). Our results suggest the coherence of soil microbial communities within and differences in communities between landscape positions in a subalpine forested watershed that reflect historical and contemporary environmental conditions.

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.

scholarly journals Associations between human impacts and forest soil microbial communities

Elem Sci Anth ◽  
2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Yongjian Chen ◽  
Jialiang Kuang ◽  
Pandeng Wang ◽  
Wensheng Shu ◽  
Albert Barberán
Keyword(s):  
Microbial Communities ◽  
Forest Soil ◽  
Human Activity ◽  
Eastern China ◽  
Soil Microbial Communities ◽  
Nitrifying Bacteria ◽  
Rrna Gene ◽  
Internal Transcribed Spacer Region ◽  
Soil Microbial ◽  
Soil Variables

We are living in a new epoch—the Anthropocene, in which human activity is reshaping global biodiversity at an unprecedented rate. Increasing efforts are being made toward a better understanding of the associations between human activity and the geographic patterns in plant and animal communities. However, similar efforts are rarely applied to microbial communities. Here, we collected 472 forest soil samples across eastern China, and the bacterial and fungal communities in those samples were determined by high-throughput sequencing of 16S rRNA gene and internal transcribed spacer region, respectively. By compiling human impact variables as well as climate and soil variables, our goal was to elucidate the association between microbial richness and human activity when climate and soil variables are taken into account. We found that soil microbial richness was associated with human activity. Specifically, human population density was positively associated with the richness of bacteria, nitrifying bacteria and fungal plant pathogens, but it was negatively associated with the richness of cellulolytic bacteria and ectomycorrhizal fungi. Together, these results suggest that the associations between geographic variations of soil microbial richness and human activity still persist when climate and soil variables are taken into account and that these associations vary among different microbial taxonomic and functional groups.

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.

scholarly journals Biocrust-forming mosses mitigate the impact of aridity on soil microbial communities in drylands: observational evidence from three continents

2018 ◽  
Vol 220 (3) ◽  
pp. 824-835 ◽  
Author(s):  
Manuel Delgado-Baquerizo ◽  
Fernando T. Maestre ◽  
David J. Eldridge ◽  
Matthew A. Bowker ◽  
Thomas C. Jeffries ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Observational Evidence ◽  
Soil Microbial ◽  
The Impact

scholarly journals Soil Heating at High Temperatures and Different Water Content: Effects on the Soil Microorganisms

Geosciences ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 355
Author(s):  
Ana Barreiro ◽  
Alba Lombao ◽  
Angela Martín ◽  
Javier Cancelo-González ◽  
Tarsy Carballas ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Water Content ◽  
Thermal Shock ◽  
Soil Microbial Communities ◽  
Initial Water Content ◽  
Initial Water ◽  
Soil Heating ◽  
Soil Microbial ◽  
Induced Changes ◽  
The Impact

Soil properties determining the thermal transmissivity, the heat duration and temperatures reached during soil heating are key factors driving the fire-induced changes in soil microbial communities. The aim of the present study is to analyze, under laboratory conditions, the impact of the thermal shock (infrared lamps reaching temperatures of 100 °C, 200 °C and 400 °C) and moisture level (0%, 25% and 50% per soil volume) on the microbial properties of three soil mixtures from different sites. The results demonstrated that the initial water content was a determinant factor in the response of the microbial communities to soil heating treatments. Measures of fire impact included intensity and severity (temperature, duration), using the degree-hours method. Heating temperatures produced varying thermal shock and impacts on biomass, bacterial activity and microbial community structure.

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

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e4178 ◽  
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.

scholarly journals Vertebrate Decomposition Is Accelerated by Soil Microbes

2014 ◽  
Vol 80 (16) ◽  
pp. 4920-4929 ◽  
Author(s):  
Christian L. Lauber ◽  
Jessica L. Metcalf ◽  
Kyle Keepers ◽  
Gail Ackermann ◽  
David O. Carter ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Soil Microbes ◽  
Soil Microbial Communities ◽  
Natural Phenomenon ◽  
Rrna Gene ◽  
Data Set ◽  
Soil Microbial ◽  
Decomposer Community ◽  
Carrion Decomposition

ABSTRACTCarrion decomposition is an ecologically important natural phenomenon influenced by a complex set of factors, including temperature, moisture, and the activity of microorganisms, invertebrates, and scavengers. The role of soil microbes as decomposers in this process is essential but not well understood and represents a knowledge gap in carrion ecology. To better define the role and sources of microbes in carrion decomposition, lab-reared mice were decomposed on either (i) soil with an intact microbial community or (ii) soil that was sterilized. We characterized the microbial community (16S rRNA gene for bacteria and archaea, and the 18S rRNA gene for fungi and microbial eukaryotes) for three body sites along with the underlying soil (i.e., gravesoils) at time intervals coinciding with visible changes in carrion morphology. Our results indicate that mice placed on soil with intact microbial communities reach advanced stages of decomposition 2 to 3 times faster than those placed on sterile soil. Microbial communities associated with skin and gravesoils of carrion in stages of active and advanced decay were significantly different between soil types (sterile versus untreated), suggesting that substrates on which carrion decompose may partially determine the microbial decomposer community. However, the source of the decomposer community (soil- versus carcass-associated microbes) was not clear in our data set, suggesting that greater sequencing depth needs to be employed to identify the origin of the decomposer communities in carrion decomposition. Overall, our data show that soil microbial communities have a significant impact on the rate at which carrion decomposes and have important implications for understanding carrion ecology.

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