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Interest in the relationships between soil microbial communities and ecosystem functions is growing with increasing recognition of the key roles microorganisms play in a variety of ecosystems. With a wealth of microbial methods now available, selecting the most appropriate method can be daunting, especially to those new to the field of microbial ec...
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... to lipid-based approaches, DNA-and RNA-based methods provide high resolution (i.e., species-specific) microbial community characterization. Here we focus on two common DNA-and RNA-based fingerprinting methods, DGGE and TRFLP analysis. Both methods exploit gene sequence variation within and between microbial species to assess community composition and diversity. Both are PCR-based, requiring nucleic acid extraction from environmental samples and subsequent PCR amplification of target genes (Fig. 3) ( Muyzer et al., 1993;Clement et al., 1998). Based on the PCR primers employed, DGGE and/ or TRFLP can assess entire bacterial, archaeal or eukaryotic communities (Feris et al., 2003;Feris et al., 2004;Cookson et al., 2007;Yergeau et al., 2007), target specific phylogenetic groups (Perez-Jimenez and Kerkhof, 2005), detect individual species ( Hristova et al., 2003) or identify specific functional groups ( Burgmann et al., 2005). Often, ribosomal DNA (rDNA) genes are targeted because they contain both highly conserved and more variable regions useful in species-level assessments of community composition ( Amann et al., ...
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... The soil biological community comprises the collective groups of all organisms in the soil environment, each inhabiting particular niches or "biomes." Among all soil communities, soil microbial communities can be characterized by various methods including physiological profiling (phenotyping) based on utilization patterns of a battery of substrates (Zak, Willig, Moorhead, & Wildman, 1994); molecular techniques based on detecting genomic sequences of DNA extracted from soil (Drenovsky, Feris, Batten, & Hristova, 2008); or biochemical analysis of cell membrane phospholipid fatty acids (PLFA) extracted from soil (Zelles, 1999). Phospholipid fatty acids analysis detects lipids of microbial membranes as "biomarkers" for specific groups of microorganisms, producing a profile or "fingerprint" of the community structure. ...
Agroforestry (AF) is an intensive land management practice where trees and shrubs are intentionally integrated into crop and livestock management practices to optimize benefits arising from biophysical interactions among the components. The five main AF practices are: riparian buffers, alley cropping, windbreaks, silvopasture, and forest farming. Due to the interactions among the components, AF provides numerous ecosystem services including soil health (SH) benefits. This chapter highlights the benefits of AF practices on SH including soil carbon (SC), physical properties, biological properties, chemical properties, decontamination, biodiversity and ecosystem services (ES) provided by improved SH of AF.
Agroforestry was approved by both the afforestation and reforestation programs and under the Clean Development Mechanisms of the Kyoto Protocol for carbon sequestration (CS). Riparian buffers reduce sediment losses, filter nutrients, retain those within the watershed, and thereby improve SH and land productivity. Windbreaks, riparian buffers, alley cropping, and silvopasture improve SC, and soil physical, chemical, and biological properties. Multi-species AF practices promote greater soil biodiversity and influence nutrient cycling, CS, decontamination, soil reactions and land productivity as compared to less diverse management practices. Adoption of agroforestry improves SH and thereby enhances supporting, provisional, regulating, and cultural ES. Although research findings are limited on SH benefits of AF for the temperate regions, existing limited literature suggests that integration of AF significantly enhances SH. In the future, data from standardized experimental designs and management plans could be extensively evaluated to identify SH indicators for developing a ranking system to use as guidelines for the establishment of AF for improved SH and ES.
... After the mining, some parts of area started to be used for agriculture; some remained as grasslands with secondary succession to forest like habitat, which resulted in this unique ecosystem, more than 10,000 years old, being destroyed. However, some peat remained in the deeper soil profile; therefore, a project into this peatbog restoration has begun in 2011, when one hundred meters of drainage ditches were blocked (Dráždil and Stanová 2012). How this measure affects peatland regeneration was carried out in our study by using several biological indicators. ...
Urban and industrial developments were the reason for draining peatlands in the past which caused changes in their ecology. Restoration of the water regime aims to bring back their original functions. This study examines the natural recovery of peatland following re-wetting, blocking the drainage ditches. We used soil microbial activity, physicochemical properties and nematode communities as indicator taxa to describe restoration status five years after management. Data were compared to those obtained from adjacent degraded forest and meadow like habitats of former peatlands. Our results indicate that re-wetting had considerable effect to soil indices and nematodes. Soil moisture and organic carbon significantly increased, while pH has not changed. In contrast, soil enzymatic activity significantly decreased after re-wetting in the restored part of the peatland compared to the degraded habitats. These conditions were probably less favourable for small metazoans, because of their abundance; species number and diversity were significantly decreased after re-wetting management. The nematode trophic structure was also significantly degraded; the restored part of peatland had less omnivore and predators as well as plant parasites. We conclude that in respect to both biological indicators and basic soil properties analysed, blocking of drainage ditches creates capable conditions for natural peatland restoration.
... In addition to Eastern Red-backed Salamanders, mesofaunal microbivores (mites and Collembola) are known to be among the mostabundant organisms in temperate forest-floor systems (Swift et al. 1979) and are therefore probably important regulators of microbes. Ecologists are increasingly recognizing the important role that soil microbes play with regard to ecosystem function, and tools are readily available to measure microbial community composition (Drenovsky et al. 2008;Chodak et al. 2016). ...
Understanding the role of species interactions as regulatory mechanisms for ecosystem processes presents a challenge to ecologists working in systems with high species diversity and habitat complexity. Recent studies suggest that interactions among intraguild predators, such as terrestrial salamanders and large arthropods, might be important for the regulation of detritivores, fungivores, and perhaps detritus within terrestrial webs. A key prediction is that interactions among predators weaken trophic cascades. Our research examined this prediction by removing predators for 4 yr from unfenced field plots to investigate the effects on litter arthropods, the microbial community, and rates of leaf litter decomposition. We manipulated predator abundance in three treatments (salamander removal, centipede removal, and multiple predator removal) compared to a control in which no predators were removed. Despite difficulties in suppressing centipede numbers, we observed increases in salamanders, millipedes, isopods, slugs, numbers of ant colonies, and gamasid mites in the centipede removal plots. Additionally, several phospholipid fatty acid markers for bacteria were suppressed in plots where salamanders were most abundant. Finally, we detected treatment effects on the rate of litter disappearance from leaf bags in our field plots: those with the most salamanders had the lowest levels of litter decomposition. Overall, we found some evidence for top-down effects of predators in a temperate forest-floor web. Our study is one of few that have employed an unfenced field design and the only study examining the effects of salamanders on forest soil microbes. The results contribute to a growing body of evidence indicating that territorial predators, such as terrestrial salamanders, can be strong regulators of species composition at lower trophic levels in a system that is commonly thought to be regulated primarily through bottom-up effects of organic matter supply.
... In addition to Eastern Red-backed Salamanders, mesofaunal microbivores (mites and Collembola) are known to be among the mostabundant organisms in temperate forest-floor systems (Swift et al. 1979) and are therefore probably important regulators of microbes. Ecologists are increasingly recognizing the important role that soil microbes play with regard to ecosystem function, and tools are readily available to measure microbial community composition (Drenovsky et al. 2008;Chodak et al. 2016). ...
Understanding the role of species interactions as regulatory mechanisms for ecosystem processes presents a challenge to ecologists working in systems with high species diversity and habitat complexity. Recent studies suggest that interactions among intraguild predators, such as terrestrial salamanders and large arthropods, might be important for the regulation of detritivores, fungivores, and perhaps detritus within terrestrial webs. A key prediction is that interactions among predators weaken trophic cascades. Our research examined this prediction by removing predators for 4 yr from unfenced field plots to investigate the effects on litter arthropods, the microbial community, and rates of leaf litter decomposition. We manipulated predator abundance in three treatments (salamander removal, centipede removal, and multiple predator removal) compared to a control in which no predators were removed. Despite difficulties in suppressing centipede numbers, we observed increases in salamanders, millipedes, isopods, slugs, numbers of ant colonies, and gamasid mites in the centipede removal plots. Additionally, several phospholipid fatty acid markers for bacteria were suppressed in plots where salamanders were most abundant. Finally, we detected treatment effects on the rate of litter disappearance from leaf bags in our field plots: those with the most salamanders had the lowest levels of litter decomposition. Overall, we found some evidence for top-down effects of predators in a temperate forest-floor web. Our study is one of few that have employed an unfenced field design and the only study examining the effects of salamanders on forest soil microbes. The results contribute to a growing body of evidence indicating that territorial predators, such as terrestrial salamanders, can be strong regulators of species composition at lower trophic levels in a system that is commonly thought to be regulated primarily through bottom-up effects of organic matter supply.
... 4,[15][16][17] However, the difficulties involved in resolving PLFA signatures of multi-species components as well as the limitation of isotopic enrichment due to the need of having a signicant amount of labelled DNA that can be separated by isotope gradient-based centrifugation may limit the global use of PLFA and DNA-based SIP strategies. 7,18 Recently, Raman spectroscopy combined with SIP has attracted a lot of attention as a tool for linking gene to function. [19][20][21] As opposed to PLFA, DNA and RNA, Raman-based SIP permits rapid, non-destructive and high throughput identication and discrimination of the bacteria responsible for metabolising labelled substrates at community and, more importantly, single cell levels. ...
... Whilst our approach does indicate that there are more bands that are isotopically labelled compared to the study carried out by Kubryk and coworkers, we do agree with these authors that stable isotopes can be highly benecial in assigning peaks to the specic vibrational modes of compounds, as illustrated in Table 1 for assigning vibrations that contain either 13 C or 15 N or both heavy isotopes. In this study we have illustrated this with 13 C and 15 N, and would expect that such an approach would work with other stable isotopes such as 18 O and 34 S, as well as other instable isotopes (e.g. 33 P), from atoms which are routinely found in metabolites and proteins within bacterial and indeed eukaryotic cells. ...
It is clear that investigating how bacterial cells work by analysing their functional roles in microbial communities is very important in environmental, clinical and industrial microbiology. The benefits of linking genes to their respective functions include reliable identification of causative agents of various diseases, which would permit appropriate and timely treatment in healthcare systems. In industrial and municipal wastewater treatment and management, such knowledge may allow for the manipulation of microbial communities, such as bioaugmentation, in order to improve the efficiency and effectiveness of bioremediation process. Stable isotope probing coupled with identification techniques has emerged to be a potentially reliable tool for discrimination, identification and characterization of bacteria at community and single cell level; knowledge which can be utilized to link microbially mediated bioprocesses to phylogeny. The development of surface-enhanced Raman scattering (SERS) technique offers an exciting alternative to the Raman and Fourier-transform infrared spectroscopic techniques in understanding metabolic processes of microorganisms in situ. SERS employing Ag and Au nanoparticles can significantly enhance the Raman signal making it an exciting candidate for the analysis of cellular components of microorganisms. In this study, Escherichia coli cells were cultivated in minimal medium containing different ratios of 12C/13C glucose and 14N/15N ammonium chloride as the only carbon and nitrogen sources respectively, with the overall final concentrations of these substrates being constant. After growth E. coli cells were analyzed with SERS employing in situ synthesis of Ag nanoparticles. This novel investigation of SERS spectral data with multivariate chemometrics demonstrated clear clusters which could be correlated to SERS spectral shifts of biomolecules from cells grown and hence labeled with 13C and 15N atoms. These shifts reflect the isotopic content of the bacteria and quantification of the isotope levels could be established using chemometrics based on partial least squares regression.
... Even so comparison between qPCR and microscopic techniques (e.g. FISH) proved a high robustness of qPCR (Baptista et al., 2014;Drenovsky et al., 2008) and most importantly, several studies have shown the usefulness of qPCR data to compare 18S rRNA pools along environmental gradients and in response to environmental changes (Liu and Gong, 2012;Marie et al., 2006;Zhu et al., 2005). ...
... Raman microscopy combined with fluorescence in-situ hybridization (FISH) and multi-isotope imaging mass spectrometry (nanoSIMS)) will further improve our understanding of soil microbial ecology (Neufeld et al., 2007). The failure to link microbial ecology to ecosystem processes is commonly related to the various scales in which these systems operate (Drenovsky et al., 2008). While microbial ecologists operate on a soil aggregate scale (0.0025 m 2 ), ecosystem functioning is described on a landscape scale (1000 m 2 ). ...
... Each of these methods has been combined with SIP to improve functional interpretations; PLFAs (Boschker et al., 1998), DNA (Radajewski et al., 2000), RNA (Manefield et al., 2002), and proteins (Jehmlich et al., 2008). All of these methods have their strengths and weaknesses, and some reviews have summarized them in the light of linking structure and functions (Torsvik and Øvreås, 2002;Drenovsky et al., 2008;Maron et al., 2011). The following review discusses the (1) the usefulness of phospholipid biomarkers to describe soil microbial communities and (2) the ability to link the microbial community to soil processes by measuring carbon stable isotope ratios in phospholipid fatty acids. ...
... In microorganisms, PLFAs are found exclusively in cell membranes and not in other parts of the cell such as storage products. Fatty acid methyl ester (FAME) analysis, which directly extracts PLFAs from soil, is a biochemical method that does not rely on culturing of microorganisms and provides information on the microbial community composition based on groupings of the fatty acids (Ibekwe and Kennedy 1998;Drenovsky et al. 2004;Drenovsky et al. 2008). PLFAs compose a relatively constant proportion of the cell biomass and signature fatty acids exist that can differentiate major taxonomic groups within a community. ...
... In microorganisms, PLFAs are found exclusively in cell membranes and not in other parts of the cell such as storage products. Fatty acid methyl ester (FAME) analysis, which directly extracts PLFAs from soil, is a biochemical method that does not rely on culturing of microorganisms and provides information on the microbial community composition based on groupings of the fatty acids (Ibekwe and Kennedy 1998;Drenovsky et al. 2004;Drenovsky et al. 2008). PLFAs compose a relatively constant proportion of the cell biomass and signature fatty acids exist that can differentiate major taxonomic groups within a community. ...
... Lotic invertebrate taxa often showed unimodal responses to the similar stressors. Four studies of wetland biodiversity were conducted showing either the change in composition of macrophytes (Emery et al., 2001) or the decrease of bacteria, vertebrates and invertebrates due to eutrophication, land use and alien species (Drenovsky et al., 2008). ...
The present review with focus on the last decade (2000–2010) aims to (i) collecting the major hypotheses explaining freshwater biodiversity pat-terns, (ii) identifying the main stressors affecting freshwater biodiversity, and (iii) revealing informa-tion gaps regarding ecosystem types, organism groups, spatial and temporal scales to highlight research needs to better propose sound conservation measures. The comparative analysis addresses six organism groups ranging from microorganisms to fish in basins, rivers, lakes, wetlands, ponds and groundwater. Short-term studies at ecoregion and catchment scale focusing on invertebrates, macrophytes and fish in Palaearctic and Nearctic regions dominated. The most frequent hypotheses tested were the landscape filter concept, the species–area relationship, the metacommunity concept. Dominating natural drivers were area, heter-ogeneity and disturbance. Land use, eutrophication and habitat destruction were identified as most important stressors. Generally, freshwater biodiversity declined in response to these stressors in contrast to increasing biodiversity determined by natural drivers across all ecosystems. Preferred organism groups were fish and invertebrates, most frequently studied in rivers, in contrast to smaller organisms (e.g. bacteria) and, e.g. groundwater being underrepresented. Hypotheses originating from the last century are still tested in freshwater research, while novel concepts are either missing or untested. Protection of freshwater biodiversity is the ultimate challenge since it supports Handling editor: Koen Martens
