Biochar soil amendment increased bacterial but decreased fungal gene abundance with shifts in community structure in a slightly acid rice paddy from Southwest China
TL;DR: The results here indicated a shift toward a bacterial dominated microbial community in the rice paddy with BSA.
About: This article is published in Applied Soil Ecology.The article was published on 2013-09-01. It has received 310 citations till now. The article focuses on the topics: Biochar & Paddy field.
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TL;DR: This review links microbial responses, including microbial activity, community structures and soil enzyme activities, with changes in soil properties caused by biochars, and summarized possible mechanisms that are involved in the effects that biochar-microbe interactions have on soil carbon sequestration and pollution remediation.
551 citations
Cites background or methods from "Biochar soil amendment increased ba..."
...To clearly interpret the microbial responses to biochar application in soils, gene copy numbers can serve as a more sensitive parameter than microbial biomass (Chen et al., 2013)....
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...…gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (TRFLP), and high-throughput sequencing (also known as next-generation sequencing, or NGS) of soil microbial genes (Chen et al., 2013; Hale et al., 2014; Kolton et al., 2011; Mackie et al., 2015; Rousk et al., 2009)....
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...Such a process is essential to explain the effects of biochar on soil remediation (Chen et al., 2013; Hale et al., 2014; Kolton et al., 2011; Mackie et al., 2015; Rousk et al., 2009)....
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...Various techniques are used to test microbial activity and community structure, including ergosterol extraction, quantitative real-time polymerase chain reaction (q-PCR), fluorescence in situ hybridization (FISH), phospholipid fatty acid quantitation (PLFA), molecular fingerprinting of 16S rRNA gene fragments including denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (TRFLP), and high-throughput sequencing (also known as next-generation sequencing, or NGS) of soil microbial genes (Chen et al., 2013; Hale et al., 2014; Kolton et al., 2011; Mackie et al., 2015; Rousk et al., 2009)....
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TL;DR: The rice straw biochar had greater potential as an amendment for reducing the bioavailability of heavy metals in soil than that of the bamboo biochar.
Abstract: Biochar is a carbon-rich solid material derived from the pyrolysis of agricultural and forest residual biomass. Previous studies have shown that biochar is suitable as an adsorbent for soil contaminants such as heavy metals and consequently re- duces their bioavailability. However, the long-term effect of dif- ferent biochars on metal extractability or soil health has not been assessed. Therefore, a 1-year incubation experiment was carried out to investigate the effect of biochar produced from bamboo and rice straw (at temperatures ≥500 °C) on the heavy metal (cadmium (Cd), copper (Cu), lead (Pb), and zinc (Zn)) extract- ability and enzyme activity (urease, catalase, and acid phospha- tase) in a contaminated sandy loam paddy soil. Three rates (0, 1, and 5 %) and two mesh sizes (<0.25 and <1 mm) of biochar applications were investigated. After incubation, the physico- chemical properties, extractable heavy metals, available phos- phorus, and enzyme activity of soil samples were analyzed. The results demonstrated that rice straw biochar significantly (P<0.05) increased the pH, electrical conductivity, and cation exchange capacity of the soil, especially at the 5 % application rate. Both bamboo and rice straw biochar significantly (P<0.05) decreased the concentration of CaCl2-extractable heavy metals as biochar application rate increased. The heavy metal extractability was significantly (P<0.01) correlated with pH, water-soluble organic carbon, and available phosphorus in soil. The 5 % appli- cation rate of fine rice straw bioc har resulted in the greatest re- ductions of extractable Cu and Zn, 97.3 and 62.2 %, respectively. Both bamboo and rice straw biochar were more effective at de- creasingextractableCu andPb thanremoving extractable Cdand Zn from the soil. Urease activity increased by 143 and 107 % after the addition of 5 % coarse and fine rice straw biochars, respectively. Both bamboo and rice straw biochars significantly (P<0.05) increased catalase activity but had no significant im- pact on acid phosphatase activity. In conclusion, the rice straw biochar had greater potential as an amendment for reducing the bioavailability of heavy metals in soil than that of the bamboo biochar. The impact of biochar treatment on heavy metal extract- ability and enzyme activity varied with the biochar type, appli- cation rate, and particle size.
405 citations
Cites background from "Biochar soil amendment increased ba..."
...Chen et al. (2013) also found that increased soil pH led to increasing alkaline phosphatase but decreasing acid phosphatase activities....
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TL;DR: Recent progresses in understanding metal-biochar interactions in soils, potential risks associated with biochar amendment, and application of biochar in soil remediation in China indicate that the remediation effect depends on the characteristics of both biochar and soil and their interactions.
362 citations
08 Apr 2019
TL;DR: In this paper, a review of the effect of biochar on soil microorganisms has received less attention than its influences on soil physicochemical properties, in particular soil carbon mineralization, nutrient cycling, and enzyme activities.
Abstract: Application of biochar to soils changes soil physicochemical properties and stimulates the activities of soil microorganisms that influence soil quality and plant performance. Studying the response of soil microbial communities to biochar amendments is important for better understanding interactions of biochar with soil, as well as plants. However, the effect of biochar on soil microorganisms has received less attention than its influences on soil physicochemical properties. In this review, the following key questions are discussed: (i) how does biochar affect soil microbial activities, in particular soil carbon (C) mineralization, nutrient cycling, and enzyme activities? (ii) how do microorganisms respond to biochar amendment in contaminated soils? and (iii) what is the role of biochar as a growth promoter for soil microorganisms? Many studies have demonstrated that biochar-soil application enhances the soil microbial biomass with substantial changes in microbial community composition. Biochar amendment changes microbial habitats, directly or indirectly affects microbial metabolic activities, and modifies the soil microbial community in terms of their diversity and abundance. However, chemical properties of biochar, (especially pH and nutrient content), and physical properties such as pore size, pore volume, and specific surface area play significant roles in determining the efficacy of biochar on microbial performance as biochar provides suitable habitats for microorganisms. The mode of action of biochar leading to stimulation of microbial activities is complex and is influenced by the nature of biochar as well as soil conditions.
336 citations
TL;DR: It is concluded that biochar is a potentially effective amendment to reverse or to prevent acidification in acid soils.
325 citations
References
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TL;DR: Version 4 of MEGA software expands on the existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses.
Abstract: We announce the release of the fourth version of MEGA software, which expands on the existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. Version 4 includes a unique facility to generate captions, written in figure legend format, in order to provide natural language descriptions of the models and methods used in the analyses. This facility aims to promote a better understanding of the underlying assumptions used in analyses, and of the results generated. Another new feature is the Maximum Composite Likelihood (MCL) method for estimating evolutionary distances between all pairs of sequences simultaneously, with and without incorporating rate variation among sites and substitution pattern heterogeneities among lineages. This MCL method also can be used to estimate transition/transversion bias and nucleotide substitution pattern without knowledge of the phylogenetic tree. This new version is a native 32-bit Windows application with multi-threading and multi-user supports, and it is also available to run in a Linux desktop environment (via the Wine compatibility layer) and on Intel-based Macintosh computers under the Parallels program. The current version of MEGA is available free of charge at (http://www.megasoftware.net).
29,021 citations
TL;DR: Analysis of the genomic DNA from a bacterial biofilm grown under aerobic conditions suggests that sulfate-reducing bacteria, despite their anaerobicity, were present in this environment.
Abstract: We describe a new molecular approach to analyzing the genetic diversity of complex microbial populations. This technique is based on the separation of polymerase chain reaction-amplified fragments of genes coding for 16S rRNA, all the same length, by denaturing gradient gel electrophoresis (DGGE). DGGE analysis of different microbial communities demonstrated the presence of up to 10 distinguishable bands in the separation pattern, which were most likely derived from as many different species constituting these populations, and thereby generated a DGGE profile of the populations. We showed that it is possible to identify constituents which represent only 1% of the total population. With an oligonucleotide probe specific for the V3 region of 16S rRNA of sulfate-reducing bacteria, particular DNA fragments from some of the microbial populations could be identified by hybridization analysis. Analysis of the genomic DNA from a bacterial biofilm grown under aerobic conditions suggests that sulfate-reducing bacteria, despite their anaerobicity, were present in this environment. The results we obtained demonstrate that this technique will contribute to our understanding of the genetic diversity of uncharacterized microbial populations.
11,380 citations
TL;DR: In this paper, a direct extraction method for measuring soil microbial biomass nitrogen (biomass N) is described, which is based on CHC13 fumigation, followed by immediate extraction with 0.5 M K2SO4 and measurement of total N released by CHC 13 in the soil extracts.
Abstract: A new “direct extraction” method for measuring soil microbial biomass nitrogen (biomass N) is described. The new method (fumigation-extraction) is based on CHC13 fumigation, followed by immediate extraction with 0.5 M K2SO4 and measurement of total N released by CHC13 in the soil extracts. The amounts of NH4-N and total N extracted by K2SO4 immediately after fumigation increased with fumigation time up to 5 days. Total N released by CHC13 after 1 day fumigation (1 day CHC13-N) and after 5 days fumigation (5 day CHC13-N) were positively correlated with the flush of mineral N (FN) in 37 soils that had been fumigated, the fumigant removed and the soils incubated for 10 days (fumigation-incubation). The regression equations were 1 day CHC13-N = (0.79 ± 0.022) FN and 5 day CHC13-N = (1.01 ± 0.027) FN, both regressions accounting for 92% of the variance in the data. In field soils previously treated with 15N-labelled fertilizer, the amounts of labelled N, measured after fumigation-extraction, were very similar to the amounts of labelled N mineralized during fumigation-incubation; both were about 4 times as heavily labelled as the soil N as a whole. These results suggest that fumigation-extraction and fumigation-incubation both measure the same fraction of the soil organic N (probably the cytoplasmic component of the soil microbial biomass) and that measurement of the total N released by CHC13 fumigation for 24 h provides a rapid method for measuring biomass N.
4,631 citations
TL;DR: Bacterial diversity was highest in neutral soils and lower in acidic soils, with soils from the Peruvian Amazon the most acidic and least diverse in this study.
Abstract: For centuries, biologists have studied patterns of plant and animal diversity at continental scales. Until recently, similar studies were impossible for microorganisms, arguably the most diverse and abundant group of organisms on Earth. Here, we present a continental-scale description of soil bacterial communities and the environmental factors influencing their biodiversity. We collected 98 soil samples from across North and South America and used a ribosomal DNA-fingerprinting method to compare bacterial community composition and diversity quantitatively across sites. Bacterial diversity was unrelated to site temperature, latitude, and other variables that typically predict plant and animal diversity, and community composition was largely independent of geographic distance. The diversity and richness of soil bacterial communities differed by ecosystem type, and these differences could largely be explained by soil pH (r(2) = 0.70 and r(2) = 0.58, respectively; P < 0.0001 in both cases). Bacterial diversity was highest in neutral soils and lower in acidic soils, with soils from the Peruvian Amazon the most acidic and least diverse in our study. Our results suggest that microbial biogeography is controlled primarily by edaphic variables and differs fundamentally from the biogeography of "macro" organisms.
4,376 citations
TL;DR: A review of the literature reveals a significant number of early studies on biochar-type materials as soil amendments either for managing pathogens, as inoculant carriers or for manipulative experiments to sorb signaling compounds or toxins as mentioned in this paper.
Abstract: Soil amendment with biochar is evaluated globally as a means to improve soil fertility and to mitigate climate change. However, the effects of biochar on soil biota have received much less attention than its effects on soil chemical properties. A review of the literature reveals a significant number of early studies on biochar-type materials as soil amendments either for managing pathogens, as inoculant carriers or for manipulative experiments to sorb signaling compounds or toxins. However, no studies exist in the soil biologyliterature that recognize the observed largevariations ofbiochar physico-chemical properties. This shortcoming has hampered insight into mechanisms by which biochar influences soil microorganisms, fauna and plant roots. Additional factors limiting meaningful interpretation of many datasets are the clearly demonstrated sorption properties that interfere with standard extraction procedures for soil microbial biomass or enzyme assays, and the confounding effects of varying amounts of minerals. In most studies, microbial biomass has been found to increase as a result of biochar additions, with significant changes in microbial community composition and enzyme activities that may explain biogeochemical effects of biochar on element cycles, plant pathogens, and crop growth. Yet, very little is known about the mechanisms through which biochar affects microbial abundance and community composition. The effects of biochar on soil fauna are even less understood than its effects on microorganisms, apart from several notable studies on earthworms. It is clear, however, that sorption phenomena, pH and physical properties of biochars such as pore structure, surface area and mineral matter play important roles in determining how different biochars affect soil biota. Observations on microbial dynamics lead to the conclusion of a possible improved resource use due to co-location of various resources in and around biochars. Sorption and therebyinactivation of growth-inhibiting substances likelyplaysa rolefor increased abundance of soil biota. No evidence exists so far for direct negative effects of biochars on plant roots. Occasionally observed decreases in abundance of mycorrhizal fungi are likely caused by concomitant increases in nutrient availability,reducing theneedfor symbionts.Inthe shortterm,therelease ofavarietyoforganic molecules from fresh biochar may in some cases be responsible for increases or decreases in abundance and activity of soil biota. A road map for future biochar research must include a systematic appreciation of different biochar-types and basic manipulative experiments that unambiguously identify the interactions between biochar and soil biota.
3,612 citations