Monitoring soil bacteria with community-level physiological profiles using Biolog™ ECO-plates in the Netherlands and Europe

Rutgers, Michiel; Wouterse, Marja; Drost, Sytske M.; Breure, A.M.; Mulder, Christian; Stone, D.; Creamer, Rachel; Winding, Anne; Bloem, J.

doi:10.1016/j.apsoil.2015.06.007

Cited by 142 publications

(76 citation statements)

References 44 publications

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“…T-RFLP and Biolog Eco Plate are both accepted methods for assessing the complexity of microbial communities in telluric environments [15,26]. However, the Biolog ® EcoPlate™ classifies the composts very differently than the T-RFLP pattern and better predicts disease suppression.…”

Section: Discussionmentioning

confidence: 99%

Alpha and Beta-diversity of Microbial Communities Associated to Plant Disease Suppressive Functions of On-farm Green Composts

et al. 2020

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Green waste composts are obtained from agricultural production chains; their suppressive properties are increasingly being developed as a promising biological control option in the management of soil-borne phytopathogens. The wide variety of microbes harbored in the compost ecological niches may regulate suppressive functions through not yet fully known underlying mechanisms. This study investigates alpha- and beta-diversity of the compost microbial communities, as indicators of the biological features. Our green composts displayed a differential pattern of suppressiveness over the two assayed pathosystems. Fungal and bacterial densities, as well as catabolic and enzyme functionalities did not correlate with the compost control efficacy on cress disease. Differences in the suppressive potential of composts can be better predicted by the variations in the community levels of physiological profiles indicating that functional alpha-diversity is more predictive than that which is calculated on terminal restriction fragments length polymorphisms (T-RFLPs) targeting the 16S rRNA gene. However, beta-diversity described by nMDS analysis of the Bray–Curtis dissimilarity allowed for separating compost samples into distinct functionally meaningful clusters and indicated that suppressiveness could be regulated by selected groups of microorganisms as major deterministic mechanisms. This study contributes to individuating new suitable characterization procedures applicable to the suppressive green compost chain.

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Section: Discussionmentioning

confidence: 99%

Alpha and Beta-diversity of Microbial Communities Associated to Plant Disease Suppressive Functions of On-farm Green Composts

et al. 2020

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“…Therefore, from an ecological perspective, it is important to determine the metabolic microbial profile in respect to contaminated soils. One of the tools appropriate for the analysis of the functional diversity of microbial communities is the community level physiological profile (CLPP) technique, also known as the BIOLOG system (Frąc et al, 2012;Garland, 1999;Rutgers et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Community-level physiological profiles of microorganisms inhabiting soil contaminated with heavy metals

Kuźniar¹,

Banach²,

Stępniewska³

et al. 2018

International Agrophysics

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A b s t r a c t. The aim of the study was to assess the differences in the bacterial community physiological profiles in soils contaminated with heavy metals versus soils without metal contaminations. The study's contaminated soil originated from the surrounding area of the Szopienice non-ferrous metal smelter (Silesia Region, Poland). The control was soil unexposed to heavy metals. Metal concentration was appraised by flame atomic absorption spectrometry, whereas the the community-level physiological profile was determined with the Biolog EcoPlates TM system. The soil microbiological activity in both sites was also assessed via dehydrogenase activity. The mean concentrations of metals (Cd and Zn) in contaminated soil samples were in a range from 147.27 to 12265.42 mg kg -1 , and the heavy metal contamination brought about a situation where dehydrogenase activity inhibition was observed mostly in the soil surface layers. Our results demonstrated that there is diversity in the physiological profiles of microorganisms inhabiting contaminated and colntrol soils; therefore, for assessment purposes, these were treated as two clusters. Cluster I included colntrol soil samples in which microbial communities utilised most of the available substrates. Cluster II incorporated contaminated soil samples in which a smaller number of the tested substrates was utilised by the contained microorganisms. The physiological profiles of microorganisms inhabiting the contaminated and the colntrol soils are distinctly different.K e y w o r d s: Biolog ECO plates, community-level physiological profiles, heavy metals

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“…Furthermore, CLPPs seem to be specific for land use, soil management and soil texture [13]. Our research showed that soil TK contents was the dominant factor affecting the microbial functional diversity in both dormant and growing seasons.…”

Section: Discussionmentioning

confidence: 91%

“…Although microorganisms are the important component for functioning of wetland ecosystem, their metabolic versatilities are poorly understood due to the complicated environmental stresses and regional microbial differentiation [12]. The Biolog EcoPlates™ is a method that relatively easy to operate, which is generally used to describe the diversity of community-level physiological profiles (CLPPs) [13–15]. Based on the biological and biochemical properties, the Biolog EcoPlates™ method can quickly characterize the ecological status of environmental samples [16], such as activated sludge [17], wastewater [18], sediments [19], and soils [13, 20].…”

Section: Introductionmentioning

confidence: 99%

Monitoring soil microorganisms with community-level physiological profiles using Biolog EcoPlates™ in Chaohu lakeside wetland, east China

Teng

Fan

Wang

et al. 2019

Preprint

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19Under the circumstance of wetland degradation, we used Biolog EcoPlates TM 20 method to investigate the impact of ecological restoration on the function of topsoil 21 microbial communities by monitoring their metabolic diversity around Chaohu lakeside 22 wetland. Four restoration patterns including reed shoaly land (RL), poplar plantation 23 land (PL), abandoned shoaly grassland (GL) and cultivated flower land (FL) were 24 selected. The result showed a rapid growth trend at the initial stage of incubation, 25 following the fastest change rate at 72 h in both dormant and growing seasons, and the 26 AWCD values of RL pattern was the highest at the detection points of each culture 27 time, while the GL were the lowest. The calculation of diversity indicators also 28 displayed significant lower McIntosh index in dormant season and Shannon-Wiener 29 index in growing season in GL than in the others (P < 0.05). Carbohydrates and 30 carboxylic acids were found to be the dominant substrates used in dormant season, 31whereas amino acids, polymers and phenolic acids were increasingly utilized by the 32 microbial communities in growing season. We observed soil total potassium as the key 33 factor that significantly affected the utilization efficiency of different carbon sources in 34 both seasons (P < 0.05). 35 Introduction 36 As one part of the terrestrial carbon pool, wetlands play a crucial role in global 37 carbon cycling process [1]. Soil is the main component of the wetland ecosystem, and 38 it can be strongly impacted by the hydrological changes caused by alternation of wetting 3 39 and drying, which alter the edaphic redox environment and thus control biogeochemical 40 processes [2]. With the development of urbanization, wetland environment has been 41 degraded resulted from agricultural reclamation, global climate change and acid 42 precipitation [3-5], which makes wetland become one of the most threatened 43 ecosystems in the world [6]. Nowadays people's awareness of ecological and 44 environmental protection has been raised, and different restoration methods have been 45 implemented to improve the wetland soil quality and species diversity. However, 46 wetland carbon sequestration is still threatened by global warming [7]. It was reported 47 that exogenous heavy metal inputs from agricultural development are introduced into 48 natural wetlands [8, 9], which may significantly affect carbon cycling and balance of 49 the area.50 In a whole wetland ecosystem, microorganisms, as the decomposer and basic agent 51 of the element circulation, play a key role in soil formation process [10, 11]. To make 52 scienti fic researches in the reconstruction and restoration of urban lakeside wetland, it 53 is necessary to explore soil microbial communities that affecting nutrient cycling and 54 functional metabolism, especially for the utilization of carbon substrates. Although 55 microorganisms are the important component for functioning of wetland ecosystem, 56 their metabolic versatilities are poorly understood due to the comp...

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Monitoring soil bacteria with community-level physiological profiles using Biolog™ ECO-plates in the Netherlands and Europe

Cited by 142 publications

References 44 publications

Alpha and Beta-diversity of Microbial Communities Associated to Plant Disease Suppressive Functions of On-farm Green Composts

Alpha and Beta-diversity of Microbial Communities Associated to Plant Disease Suppressive Functions of On-farm Green Composts

Community-level physiological profiles of microorganisms inhabiting soil contaminated with heavy metals

Monitoring soil microorganisms with community-level physiological profiles using Biolog EcoPlates™ in Chaohu lakeside wetland, east China

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