Microbial diversity and soil functions Nannipieri, P.; Ascher, J.; Ceccherini, M. T. ...
European journal of soil science,
January 2017, 2017-01-00, 20170101, Letnik:
68, Številka:
1
Journal Article
Recenzirano
Summary
Soil is a complex and dynamic biological system, and still in 2003 it is difficult to determine the composition of microbial communities in soil. We are also limited in the determination of ...microbially mediated reactions because present assays for determining the overall rate of entire metabolic processes (such as respiration) or specific enzyme activities (such as urease, protease and phosphomonoesterase activity) do not allow any identification of the microbial species directly involved in the measured processes. The central problem posed by the link between microbial diversity and soil function is to understand the relations between genetic diversity and community structure and between community structure and function. A better understanding of the relations between microbial diversity and soil functions requires not only the use of more accurate assays for taxonomically and functionally characterizing DNA and RNA extracted from soil, but also high‐resolution techniques with which to detect inactive and active microbial cells in the soil matrix.
Soil seems to be characterized by a redundancy of functions; for example, no relationship has been shown to exist between microbial diversity and decomposition of organic matter. Generally, a reduction in any group of species has little effect on overall processes in soil because other microorganisms can take on its function.
The determination of the composition of microbial communities in soil is not necessary for a better quantification of nutrient transformations. The holistic approach, based on the division of the systems in pools and the measurement of fluxes linking these pools, is the most efficient. The determination of microbial C, N, P and S contents by fumigation techniques has allowed a better quantification of nutrient dynamics in soil. However, further advances require determining new pools, such as active microbial biomass, also with molecular techniques. Recently investigators have separated 13C‐ and 12C‐DNA, both extracted from soil treated with a 13C source, by density‐gradient centrifugation. This technique should allow us to calculate the active microbial C pool by multiplying the ratio between labelled and total DNA by the microbial biomass C content of soil. In addition, the taxonomic and functional characterization of 13C‐DNA allows us to understand more precisely the changes in the composition of microbial communities affected by the C‐substrate added to soil.
The review discusses origin, state and function of extracellular DNA in soils and sediments. Extracellular DNA can be released from prokaryotic and eukaryotic cells and can be protected against ...nuclease degradation by its adsorption on soil colloids and sand particles. Laboratory experiments have shown that DNA adsorbed by colloids and sand particles can be taken up by prokaryotic competent cells and be involved in natural transformation. Most of these experiments have been carried out under artificial conditions with pure DNA molecules and pure adsorbing matrices, but in soils and sediments, pure surface-reactive colloids are not present and DNA is present with other cellular components (wall debris, proteins, lipids, RNA, etc.) especially if released after cell lysis. The presence of inorganic compounds and organic molecules on both soil particles and DNA molecules can influence the DNA adsorption, degradation and transformation of competent cells. Extracellular DNA can be used as C, N and P sources by heterotrophic microorganisms and plays a significant role in bacterial biofilm formation. The nucleotides and nucleosides originated from the degradation of extracellular DNA can be re-assimilated by soil microorganisms. Extracellular DNA in soil can be leached and moved by water through the soil profile by capillarity. In this way, the extracellular DNA secreted by a cell can reach a competent bacterial cell far from the donor cell. Finally, the characterisation of extracellular DNA can integrate information on the composition of the microbial community of soil and sediments obtained by analysing intracellular DNA.
Wild bees provide vital pollination services for many native and agricultural plant species, yet the landscape conditions needed to support wild bee populations are not well understood or ...appreciated. We assessed the influence of landscape composition on bee abundance and species richness in apple (Malm spp.) orchards of northeastern Wisconsin during the spring flowering period. A diverse community of bee species occurs in these apple orchards, dominated by wild bees in the families Andrenidae and Halictidae and the honey bee, Apis mellifera L. Proportion of forest area in the surrounding landscape was a significant positive predictor of wild bee abundance in orchards, with strongest effects at a GIS (Geographic Information Systems) buffer distance of 1,000 m or greater. Forest area also was positively associated with species richness, showing strongest effects at a buffer distance of 2,000 m. Nonagricultural developed land (homes, lawns, etcetera) was significantly negatively associated with species richness at buffer distances >750 m and wild bee abundance in bowl traps at all distances. Other landscape variables statistically associated with species richness or abundance of wild bees included proportion area of pasture (positive) and proportion area of roads (negative). Forest area was not associated with honey bee abundance at any buffer distance. These results provide clear evidence that the landscape surrounding apple orchards, especially the proportion of forest area, affects richness and abundance of wild bees during the spring flowering period and should be a part of sustainable land management strategies in agro-ecosystems of northeastern Wisconsin and other apple growing regions.
Microbial diversity and soil functions Nannipieri, P.; Ascher, J.; Ceccherini, M. T. ...
European journal of soil science,
December 2003, Letnik:
54, Številka:
4
Journal Article
Recenzirano
Summary
Soil is a complex and dynamic biological system, and still in 2003 it is difficult to determine the composition of microbial communities in soil. We are also limited in the determination of ...microbially mediated reactions because present assays for determining the overall rate of entire metabolic processes (such as respiration) or specific enzyme activities (such as urease, protease and phosphomonoesterase activity) do not allow any identification of the microbial species directly involved in the measured processes. The central problem posed by the link between microbial diversity and soil function is to understand the relations between genetic diversity and community structure and between community structure and function. A better understanding of the relations between microbial diversity and soil functions requires not only the use of more accurate assays for taxonomically and functionally characterizing DNA and RNA extracted from soil, but also high‐resolution techniques with which to detect inactive and active microbial cells in the soil matrix.
Soil seems to be characterized by a redundancy of functions; for example, no relationship has been shown to exist between microbial diversity and decomposition of organic matter. Generally, a reduction in any group of species has little effect on overall processes in soil because other microorganisms can take on its function.
The determination of the composition of microbial communities in soil is not necessary for a better quantification of nutrient transformations. The holistic approach, based on the division of the systems in pools and the measurement of fluxes linking these pools, is the most efficient. The determination of microbial C, N, P and S contents by fumigation techniques has allowed a better quantification of nutrient dynamics in soil. However, further advances require determining new pools, such as active microbial biomass, also with molecular techniques. Recently investigators have separated 13C‐ and 12C‐DNA, both extracted from soil treated with a 13C source, by density‐gradient centrifugation. This technique should allow us to calculate the active microbial C pool by multiplying the ratio between labelled and total DNA by the microbial biomass C content of soil. In addition, the taxonomic and functional characterization of 13C‐DNA allows us to understand more precisely the changes in the composition of microbial communities affected by the C‐substrate added to soil.
•We set up a culture-independent assessment of soil microbial biomass.•PicoGreen quantification of crude dsDNA extracts provides reliable data.•The method is simple, high-throughput, and does not ...require expensive equipment.
We set up a simple, culture independent, low-cost and high-throughput method for DNA-based quantitative assessment of soil microbial biomass using eight soils covering a wide range of physico-chemical properties. DNA was extracted with a 0.12M, pH 8 Na2HPO4 buffer using bead beating; double stranded DNA (dsDNA) was quantified in a crude (not purified) extract using PicoGreen reagent. In contrast to yields obtained by using a commercial standard method (FastDNA Kit for soil, MP-Biomedicals), our yields of dsDNA were generally higher, most probably because any purification method for obtaining highly pure DNA for downstream analyses leads to DNA loss. These results suggest the new method provides more reliable quantitative data; thus it is a good environmental indicator, as an underestimation of the soil microbial biomass due to DNA loss during purification can be excluded. The ratio between microbial C (Cmic) obtained by the traditional, widely used fumigation-extraction method and dsDNA ranged from 12.0 to 63.5μg Cmic per μg dsDNA. Crude DNA obtained by the new method as well as purified DNA obtained by using the commercial kit were compared in terms of quantity (fluorometry; spectrophotometry) and quality (purity indices: A260/A280, A260/A230; PCR compatibility; gel electrophoresis: molecular weight and molecular integrity). Our results suggest that the new method provides a high-throughput estimator of microbial biomass (expressed as μgdsDNAg−1 soil) in soils having widely different properties without the need for high-cost commercial extraction kits and/or cumbersome individual methods. Due to its simplicity, speed and low-cost, our method is capable for routine quantitative assessments of soil microbial biomass, assessable also for soil scientists with laboratories that are otherwise not equipped for molecular analyses.
To describe the decay stage of coarse woody debris (CWD) a five decay-class system has been introduced and it is currently the most commonly applied. This system is based on visual, geometric and ...tactile features of the wood in the field; however, a detailed chemical characterization is often missing. Furthermore, the driving mechanisms (particularly substrate quality vs. environmental conditions) of deadwood decay are controversially discussed. Consequently, we investigated how typical major and minor chemical parameters of wood were correlated with the decay stage. The decomposition patterns of Norway spruce (Picea abies (L.) Karst) and European larch (Larix decidua Mill.) CWD of an Alpine setting were analyzed, and how the chemical and physical parameters were affected by the substrate and environmental conditions was checked. Two altitudinal sequences, having a different exposure (north- vs. south-facing sites), were sampled. We measured main biochemical compounds (lignin and cellulose), physical properties (density and water content), element concentrations (C, N, P, K, Ca, Mg, Fe, Mn), and the carbon isotopic signature (δ13C) of living trees and CWD at five decomposition stages (decay classes). Most investigated wood physico-chemical parameters such as wood density, water content, lignin and cellulose and even minor constituents (N, Ca, Mg, P, Fe, Mn) correlated well to the five decay-class system. Some important components, such as the carbon concentration and δ13C, did not vary with increasing decomposition. Our hypothesis that the different substrate should be traceable during CWD decay had to be rejected, although some statistically significant chemical differences between larch and spruce were measured in the living trees. The chosen tree species were probably not different enough to be chemically traceable in the CWD. Already in decay class 1, these differences were zeroed. The site conditions (expressed by the different altitudes and exposure) influenced only some of the investigated parameters, namely lignin, the δ13C isotopic ratio and nutrients such as P, Ca and K.
Bluegill Lepomis macrochirus showed variation in their diet and trophic morphology based on habitat. Pelagic L. macrochirus feed almost exclusively on cladocerans; littoral L. macrochirus feed on a ...variety of benthic invertebrates, molluscs, cladocerans and insects. Fish from the littoral habitat had wider pharyngeal jaws, which probably allowed them to crush gastropods and process benthic invertebrates.
This study focuses on the biological and morphological development of humus profiles in forested Italian Alpine soils as a function of
climate
. Humus form description, systematic investigation of ...microannelid communities and polyphasic biochemical fingerprinting of soil microbial communities (denaturing gradient gel electrophoresis (DGGE) and phospholipid fatty acid analysis (PLFA)) were performed to compare sites differing in mean annual temperature due to different altitude and exposure. Although the soil biota showed complex responses, several differences in soil biological properties seem to be due to thermal differences. Although soil acidity also determines biological properties, it is not a state factor but rather influenced by them. The thickness of the organic layer and the acidification of the subjacent mineral horizon increased under cooler conditions (north-exposure; higher altitude), whereas the thickness of the A horizon inversely decreased. Species richness of microannelid assemblages was higher under warmer conditions (south-exposure; lower altitude) and the vertical distribution of microannelids shifted along the gradient to lower temperatures from predominant occurrence in the mineral soil to exclusive occurrence in the organic layer. Microbial biomass (total PLFA) was higher at the cooler sites; the prevalence of Gram-negative bacteria could be ascribed to their better adaptation to lower temperature, pH and nutrient contents. The δ
13
C signatures of the PLFA markers suggested a lower decomposition rate at the cooler sites, resulting in a lower respiratory loss and an accumulation of weakly decomposed organic material. DGGE data supported the PLFA results. Both parameters reflected the expected thermal sequence. This multidisciplinary case study provided indications of an association of
climate
, mesofauna and microbiota using the humus form as an overall link. More data are however needed and further investigations are encouraged.
Beringite (B) and zerovalent iron grit (Z), singly and in combination (BZ), were added to a loamy sand soil contaminated by trace elements (Reppel, Belgium), mainly by arsenic (As), to reduce As ...labile fractions and phytoavailability. An uncontaminated sandy soil was studied for comparison. Soils were placed in large lysimeters cultivated with maize and vegetables for 6 years. pH, organic C and total N content increased in amended soils. The Z and BZ treatments reduced the Ca(NO
3)
2
− extractable soil As and As uptake by lettuce. The BZ lettuces had also the lowest foliar Pb, Cd, Zn, and Mn concentrations. All amendments had positive effects on the soil microbial biomass and reduced the qCO
2. Glucose mineralization was increased in Z and BZ amended soils. Acid phosphomonoesterase activity was higher in the untreated soil than in the other soils; the alkaline phosphomonoesterase, phosphodiesterase and protease activities were increased by Z and BZ treatments, whereas B amendment had less positive effects. Genetic fingerprinting using Denaturing Gradient Gel Electrophoresis (DGGE) revealed shifts in the composition of eubacterial and fungal communities of the amended soils. Microbial species richness decreased rather than increased in the treated soils, regardless of reduced trace element availability and increased soil microbial biomass and activity.
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