scholarly journals Soil microbial community structure and diversity are largely influenced by soil pH and nutrient quality in 78-year-old tree plantations

2017 ◽  
Author(s):  
Xiaoqi Zhou ◽  
Zhiying Guo ◽  
Chengrong Chen ◽  
Zhongjun Jia
Keyword(s):  
Community Structure ◽  
Soil Ph ◽  
Tree Species ◽  
Diversity Indices ◽  
Slash Pine ◽  
Tree Plantations ◽  
Nutrient Quality ◽  
Soil Microbial ◽  
Hoop Pine ◽  
Soil Bacterial

Abstract. Forest plantations have been recognized as a key strategy management tool for stocking carbon (C) in soils, thereby contributing to climate warming mitigation. However, long-term ecological consequences of anthropogenic forest plantations on the community structure and diversity of soil microorganisms and the underlying mechanisms determining these patterns are poorly understood. In this study, we selected 78-year-old tree plantations that included three coniferous tree species (i.e., slash pine, hoop pine and kauri pine) and an eucalypt species in subtropical Australia. We investigated the patterns of community structure, and the diversity of soil bacteria and eukaryotes by using high-throughput sequencing of 16S rRNA and 18S rRNA genes. We also measured the potential methane oxidation capacity under different tree species. The results showed that slash pine and Eucalyptus significantly increased the dominant taxa of bacterial Acidobacteria and the dominant taxa of eukaryotic Ascomycota, and formed clusters of soil bacterial and eukaryotic communities, which were clearly different from the clusters under hoop pine and kauri pine. Soil pH and nutrient quality indicators such as C : nitrogen (N) and extractable organic C : extractable organic N were key factors determining the patterns of soil bacterial and eukaryotic communities among the different tree species treatments. Slash pine and Eucalyptus had significantly lower soil bacterial and eukaryotic operational taxonomical unit numbers and lower diversity indices than kauri pine and hoop pine. A key factor limitation hypothesis was introduced, which gives a reasonable explanation for lower diversity indices under slash pine and Eucalyptus. In addition, slash pine and Eucalyptus had a higher soil methane oxidation capacity than the other tree species. These results suggest that significant changes in soil microbial communities may occur in response to chronic disturbance by tree plantations, and highlight the importance of soil pH and physiochemical characteristics in microbially-mediated ecological processes in forested soils.

scholarly journals Soil microbial community structure and diversity are largely influenced by soil pH and nutrient quality in 78-year-old tree plantations

2017 ◽  
Vol 14 (8) ◽  
pp. 2101-2111 ◽  
Author(s):  
Xiaoqi Zhou ◽  
Zhiying Guo ◽  
Chengrong Chen ◽  
Zhongjun Jia
Keyword(s):  
Community Structure ◽  
Soil Ph ◽  
Tree Species ◽  
Diversity Indices ◽  
Slash Pine ◽  
Tree Plantations ◽  
Nutrient Quality ◽  
Soil Microbial ◽  
Hoop Pine ◽  
Soil Bacterial

Abstract. Forest plantations have been recognised as a key strategy management tool for stocking carbon (C) in soils, thereby contributing to climate warming mitigation. However, long-term ecological consequences of anthropogenic forest plantations on the community structure and diversity of soil microorganisms and the underlying mechanisms in determining these patterns are poorly understood. In this study, we selected 78-year-old tree plantations that included three coniferous tree species (i.e. slash pine, hoop pine and kauri pine) and a eucalypt species in subtropical Australia. We investigated the patterns of community structure, and the diversity of soil bacteria and eukaryotes by using high-throughput sequencing of 16S rRNA and 18S rRNA genes. We also measured the potential methane oxidation capacity under different tree species. The results showed that slash pine and Eucalyptus significantly increased the dominant taxa of bacterial Acidobacteria and the dominant taxa of eukaryotic Ascomycota, and formed clusters of soil bacterial and eukaryotic communities, which were clearly different from the clusters under hoop pine and kauri pine. Soil pH and nutrient quality indicators such as C : nitrogen (N) and extractable organic C : extractable organic N were key factors in determining the patterns of soil bacterial and eukaryotic communities between the different tree species treatments. Slash pine and Eucalyptus had significantly lower soil bacterial and eukaryotic operational taxonomical unit numbers and lower diversity indices than kauri pine and hoop pine. A key factor limitation hypothesis was introduced, which gives a reasonable explanation for lower diversity indices under slash pine and Eucalyptus. In addition, slash pine and Eucalyptus had a higher soil methane oxidation capacity than the other tree species. These results suggest that significant changes in soil microbial communities may occur in response to chronic disturbance by tree plantations, and highlight the importance of soil pH and physiochemical characteristics in microbially mediated ecological processes in forested soils.

scholarly journals Community Structure Analyses Are More Sensitive to Differences in Soil Bacterial Communities than Anonymous Diversity Indices

2006 ◽  
Vol 72 (12) ◽  
pp. 7804-7812 ◽  
Author(s):  
Martin Hartmann ◽  
Franco Widmer
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Rflp Analysis ◽  
Diversity Indices ◽  
Soil Bacterial Community ◽  
Community Structures ◽  
Soil Microbial ◽  
Soil Bacterial

ABSTRACT Changes in the diversity and structure of soil microbial communities may offer a key to understanding the impact of environmental factors on soil quality in agriculturally managed systems. Twenty-five years of biodynamic, bio-organic, or conventional management in the DOK long-term experiment in Switzerland significantly altered soil bacterial community structures, as assessed by terminal restriction fragment length polymorphism (T-RFLP) analysis. To evaluate these results, the relation between bacterial diversity and bacterial community structures and their discrimination potential were investigated by sequence and T-RFLP analyses of 1,904 bacterial 16S rRNA gene clones derived from the DOK soils. Standard anonymous diversity indices such as Shannon, Chao1, and ACE or rarefaction analysis did not allow detection of management-dependent influences on the soil bacterial community. Bacterial community structures determined by sequence and T-RFLP analyses of the three gene libraries substantiated changes previously observed by soil bacterial community level T-RFLP profiling. This supported the value of high-throughput monitoring tools such as T-RFLP analysis for assessment of differences in soil microbial communities. The gene library approach also allowed identification of potential management-specific indicator taxa, which were derived from nine different bacterial phyla. These results clearly demonstrate the advantages of community structure analyses over those based on anonymous diversity indices when analyzing complex soil microbial communities.

scholarly journals Agricultural practice negatively affects soil microbial diversity and nitrogen functional genes comparing to adjacent native forest soils

2021 ◽  
Author(s):  
Tiehang Wu ◽  
Michael Sabula ◽  
Holli Milner ◽  
Gary Strickland ◽  
Gan Liu
Keyword(s):  
Community Structure ◽  
Bacterial Diversity ◽  
Forest Soils ◽  
Agricultural Practices ◽  
Functional Genes ◽  
Agricultural Practice ◽  
Soil Bacterial Diversity ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Soil Bacterial

Soil microbial diversity and community are determined by anthropogenic activities and environmental conditions, which greatly affect the functioning of ecosystem. We investigated the soil bacterial diversity, communities, and nitrogen (N) functional genes with different disturbance intensity levels from crop, transition, to forest soils at three locations in the coastal region of Georgia, USA. Illumina high-throughput DNA sequencing based on bacterial 16S rRNA genes were performed for bacterial diversity and community analyses. Nitrifying (AOB amoA) and denitrifying (nirK) functional genes were further detected using quantitative PCR (qPCR) and Denaturing Gradient Gel Electrophoresis (DGGE). Soil bacterial community structure determined by Illumina sequences were significantly different between crop and forest soils (p < 0.01), as well as between crop and transition soils (p = 0.01). However, there is no difference between transition and forest soils. Compared to less disturbed forest, agricultural practice significantly decreased soil bacterial richness and Shannon diversity. Soil pH and nitrate contents together contributed highest for the observed different bacterial communities (Correlations = 0.381). Two OTUs (OTU5, OTU8) belonging to Acidobacteriales species decreased in crop soils, however, agricultural practices significantly increased an OTU (OTU4) of Nitrobacteraceae. The relative abundance of AOB amoA gene was significantly higher in crop soils than in forest and transition soils. Distinct grouping of soil denitrifying bacterial nirK communities was observed and agricultural practices significantly decreased the diversity of nirK gene compared to forest soils. Anthropogenic effects through agricultural practices negatively affecting the soil bacterial diversity, community structure, and N functional genes.

The influence of light on soil community structure and consequences for soil CO2, CO18O and COS exchange

2020 ◽  
Author(s):  
Lisa Wingate ◽  
Clement Foucault ◽  
Nicolas Fanin ◽  
Joana Sauze ◽  
Pierre-Alain Maron ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Soil Ph ◽  
Isotope Composition ◽  
Light Availability ◽  
Alkaline Soils ◽  
Soil Microbial ◽  
Microbial Groups ◽  
Taxonomic Groups ◽  
Carbonyl Sulphide

&lt;p&gt;The stable oxygen isotope composition of atmospheric CO&lt;sub&gt;2&lt;/sub&gt; and the mixing ratio of carbonyl sulphide (COS) are potential tracers of biospheric CO&lt;sub&gt;2&lt;/sub&gt; fluxes at large scales. However, the use of these tracers hinges on our ability to understand and better predict the activity of the enzyme carbonic anhydrase (CA) in different soil microbial groups, including phototrophs. Because different classes of the CA family (&amp;#945;, &amp;#946; and &amp;#947;) may have different affinities to CO&lt;sub&gt;2&lt;/sub&gt; and COS and their expression should also vary between different microbial groups, differences in the community structure could impact the &amp;#8216;community-integrated&amp;#8217; CA activity differently for CO&lt;sub&gt;2&lt;/sub&gt; and COS. Four soils of different pH were incubated in the dark or with a diurnal cycle for forty days to vary the abundance of native phototrophs. Fluxes of CO&lt;sub&gt;2&lt;/sub&gt;, CO&lt;sup&gt;18&lt;/sup&gt;O and COS were measured to estimate CA activity alongside the abundance of bacteria, fungi and phototroph genes. The abundance of soil phototrophs increased most at higher soil pH. In the light, the strength of the soil CO&lt;sub&gt;2&lt;/sub&gt; sink and the CA-driven CO&lt;sub&gt;2&lt;/sub&gt;-H&lt;sub&gt;2&lt;/sub&gt;O isotopic exchange rates correlated with phototroph abundance. COS uptake rates were attributed to fungi whose abundance was positively enhanced in alkaline soils but only in the presence of increased phototrophs. In addition we developed a metabarcoding approach to reveal the interactions of specific taxonomic groups incuding photosynthetic eukaryotic algae and cyanobacteria when exposed to light and their impact on flux rates. Our findings demonstrate that soil-atmosphere CO&lt;sub&gt;2&lt;/sub&gt;, COS and CO&lt;sup&gt;18&lt;/sup&gt;O fluxes are strongly regulated by the microbial community structure in response to changes in soil pH and light availability and support the idea that different members of the microbial community express different classes of CA, with different affinities to CO&lt;sub&gt;2&lt;/sub&gt; and COS.&lt;/p&gt;

scholarly journals Liming Alters the Soil Microbial Community and Extracellular Enzymatic Activities in Temperate Coniferous Forests

Forests ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 190
Author(s):  
Sangsub Cha ◽  
Yong Suk Kim ◽  
Ah Lim Lee ◽  
Dong-Hyeon Lee ◽  
Namin Koo
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Biomass ◽  
Bacterial Community ◽  
Soil Ph ◽  
Fungal Community ◽  
Anthropogenic Activities ◽  
Soil Microbial Communities ◽  
Lime Treatment ◽  
Soil Microbial

Soil acidification caused by anthropogenic activities adversely affects forest ecosystems by altering soil pH, which is an important factor in soil quality and function. Liming is one suggested way to solve this problem. This study was performed to evaluate the effects of liming in acidic forest soils by determining soil microbial biomass, microbial community structure, and extracellular enzyme activities associated with carbon, nitrogen, and phosphorus cycling. Lime treatment increased soil pH by up to 40%, significantly increased organic matter (OM) content at some sites, and altered the enzyme activity of the soil. With liming, the microbial biomass appeared to be affected by the chemical properties of the soil, such as pH, Ca2+, Mg2+, K+, and exchangeable aluminum (Ale) levels, although there were no significant differences at the site level. Enzymatic activity was found to be affected by pH, Ca2+, Mg2+, electrical conductivity (EC), and Ale; and acid phosphatase (AP) and phenol oxidase (POX) activity were significantly affected by lime treatment. AP activity decreased from 0.62 to 0.66, and POX activity increased from 1.75 to 3.00 in part of the sites. The bacterial community richness was influenced by pH as a direct effect of lime treatment. The fungal community richness was associated with changes in K+ that were not due to lime treatment. The bacterial community structure was affected by soil OM, total nitrogen (TN), pH, and Ca2+; and the fungal community structure was affected by pH, Mg2+, and K+. In conclusion, changes in soil environmental conditions by liming can affect soil microbial communities and functions through direct or indirect processes, further changing ecosystem processes.

scholarly journals Agricultural practice altering soil microbial diversity and nitrogen functional genes comparing to adjacent native forest soils

2021 ◽  
Author(s):  
Tiehang Wu ◽  
Michael Sabula ◽  
Holli Milner ◽  
Gary Strickland ◽  
Gan Liu
Keyword(s):  
Community Structure ◽  
Bacterial Diversity ◽  
Forest Soils ◽  
Agricultural Practices ◽  
Functional Genes ◽  
Agricultural Practice ◽  
Soil Bacterial Diversity ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Soil Bacterial

Soil microbial diversity and community are determined by anthropogenic activities and environmental conditions, which greatly affect the functioning of ecosystem. We investigated the soil bacterial diversity, communities, and nitrogen (N) functional genes with different disturbance intensity levels from crop, transition, to forest soils at three locations in the coastal region of Georgia, USA. Illumina high-throughput DNA sequencing based on bacterial 16S rRNA genes were performed for bacterial diversity and community analyses. Nitrifying (AOB amoA) and denitrifying (nirK) functional genes were further detected using quantitative PCR (qPCR) and Denaturing Gradient Gel Electrophoresis (DGGE). Soil bacterial community structure determined by Illumina sequences were significantly different between crop and forest soils (p < 0.01), as well as between crop and transition soils (p = 0.01). However, there is no difference between transition and forest soils. Compared to less disturbed forest, agricultural practice significantly decreased soil bacterial richness and Shannon diversity. Soil pH and nitrate contents together contributed highest for the observed different bacterial communities (Correlations = 0.381). Two OTUs (OTU5, OTU8) belonging to Acidobacteriales species decreased in crop soils, however, agricultural practices significantly increased an OTU (OTU4) of Nitrobacteraceae. The relative abundance of AOB amoA gene was significantly higher in crop soils than in forest and transition soils. Distinct grouping of soil denitrifying bacterial nirK communities was observed and agricultural practices significantly decreased the diversity of nirK gene compared to forest soils. Anthropogenic effects through agricultural practices negatively affecting the soil bacterial diversity, community structure, and N functional genes.

scholarly journals Bacterial Community in Soils Following Century-Long Application of Organic or Inorganic Fertilizers under Continuous Winter Wheat Cultivation

Agronomy ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 1497
Author(s):  
Xiufen Li ◽  
Shiping Deng ◽  
William R. Raun ◽  
Yan Wang ◽  
Ying Teng
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Winter Wheat ◽  
Soil Ph ◽  
Bacterial Community Structure ◽  
Critical Role ◽  
Soil Bacterial Community ◽  
Inorganic Fertilizers ◽  
Relative Abundances ◽  
Soil Bacterial

Fertilization is one of the most common agricultural practices to achieve high yield. Although microbes play a critical role in nutrient cycling and organic matter decomposition, knowledge of the long-term responses of the soil bacterial community to organic and inorganic fertilizers is still limited. This study was conducted to evaluate the effects of century-long organic (manure), inorganic (NPK), and no fertilization (control) treatments on soil bacterial community structure under continuous winter wheat (Triticum aestivum L.) cultivation. Fertilization treatments altered the richness, diversity and composition of the soil bacterial community. Compared with the control, manure significantly increased the operational taxonomic units (OTUs), Chao 1 and Shannon indices, and taxonomic groups, while NPK significantly decreased these parameters. Fertilization treatments did not alter the types of dominant phyla but did significantly affect their relative abundances. Acidobacteria and Proteobacteria were the most dominant phyla in all treatments. Manure led to enrichment of most phyla, with a diazotrophic group, Cyanobacteria, being an exception; NPK reduced most phyla, but enriched Chloroflexi; control led to promotion of Cyanobacteria. Soil pH and NO3− were two dominant parameters influencing the bacterial community structure. Soil pH positively correlated with the relative abundances of Proteobacteria and Gemmatimonadetes but negatively correlated with those of Acidobacteria and Chloroflexi; NO3− negatively correlated with the relative abundance of Cyanobacteria, which was 14–52 times higher in control than the fertilized soils. Cyanobacteria, especially M. paludosus and L. appalachiana, could be the key players in maintaining wheat productivity in the century-long unfertilized control.

scholarly journals Changes in Soil Microbial Community Structure Following Different Tree Species Functional Traits Afforestation

Forests ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1018
Author(s):  
Yang Gao ◽  
Xiuwei Wang ◽  
Zijun Mao ◽  
Liu Yang ◽  
Zhiyan Jiang ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Functional Traits ◽  
Microbial Community Structure ◽  
Tree Species ◽  
Soil Microbial Community ◽  
Soil Microbial Community Structure ◽  
Carbon And Nitrogen ◽  
Soil Microbial ◽  
Microbial Community Structures

The soil microbial community structure is critical to the cycling of carbon and nitrogen in forest soils. As afforestation practices increasingly promote different functional traits of tree species, it has become critical to understand how they influence soil microbial community structures, which directly influence soil biogeochemical processes. We used fungi ITS and bacteria 16S rDNA to investigate soil microbial community structures in three monoculture plantations consisting of a non-native evergreen conifer (Pinus sibirica), a native deciduous conifer (Larix gmelinii), and a native deciduous angiosperm (Betula platyphylla) and compared them with two 1:1 mixed-species plantations (P. sibirica and L. gmelinii, P. sibirica and B. platyphylla). The fungal community structure of the conifer–angiosperm mixed plantation was similar to that of the non-native evergreen conifer, and the bacterial community structure was similar to that of the angiosperm monoculture plantation. Fungal communities were strongly related to tree species, but bacterial communities were strongly related to soil nitrogen. The co-occurrence networks were more robust in the mixed plantations, and the microbial structures associated with soil carbon and nitrogen were significantly increased. Our results provide a comparative study of the soil microbial ecology in response to afforestation of species with different functional traits and enhance the understanding of factors controlling the soil microbial community structure.

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