scholarly journals Effects of Thinning on Microbial Community Structure in the Organic Horizon of Chinese Pine Plantations in Badaling, Beijing, China

Forests ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 828 ◽  
Author(s):  
Wang ◽  
Zhao ◽  
Sun ◽  
Yang ◽  
Zhou
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Organic Carbon ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Pine Plantations ◽  
Pinus Tabulaeformis ◽  
Organic Horizon ◽  
Moderate Intensity ◽  
Chinese Pine

Research Highlights: Moderate thinning can effectively improve forestry production and change the microenvironment of understory vegetation. Background and Objectives: Microbial communities control the decomposition and transformation of forest organic matter; however, the influence of thinning on microbes in the organic horizon remains unclear. Materials and Methods: In this study, we subjected four plots of Chinese pine plantations in Badaling, Beijing to different thinning intensities, including no thinning (T0), low-intensity thinning (T10), medium-intensity thinning (T20), and high-intensity thinning (T50). The changes in chemical properties and microbial community compositions observed in the organic horizon, which comprised undecomposed litter (L layer) and half-decomposed litter (F layer), were analyzed after thinning. Microbial community compositions were evaluated using phospholipid fatty acid (PLFA) methods. Results: The results showed that the abundances of gram-negative bacteria (GN) and total bacteria (B) under the T10 thinning condition were the highest among the four thinning intensities, and the abundance of arbuscular mycorrhizal fungi (AMF) in T20 was higher than under other thinning intensities. The abundance of gram-positive bacteria (GP) and actinobacteria (ACT) in T10 was lower than in both T0 and T50. The abundance of total PLFAs and fungi (FU) was higher in the L layer, whereas the abundance of GP, GN, B, ACT, and AMF was higher in the F layer. Conclusions: Our results demonstrated that the L layer better reflects the influence of thinning on litter. Redundancy analysis (RDA) results indicated that the organic carbon (LOC) , dissolved organic carbon (DOC), and ammonium nitrogen (NH4+-N)contents of litter were primarily responsible for the observed changes in microbial community structure, with LOC alone explaining 62.6% of the total variance among the litter substrate factors selected. Overall, moderate-intensity thinning of Pinus tabulaeformis Carr. plantations created more favorable conditions for microbial communities in the organic horizon.

Phylum-Specific Primer Design and Implication in Quantification of the Microbial Community Structure in GuJingGong Pit Mud

2014 ◽  
Vol 1051 ◽  
pp. 311-316 ◽  
Author(s):  
Xi Mei Luo ◽  
Zhi Lei Gao ◽  
Hui Min Zhang ◽  
An Jun Li ◽  
Hong Kui He ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Real Time Quantitative Pcr ◽  
Sequencing Technologies ◽  
Specific Pcr ◽  
Pit Mud ◽  
Almost All ◽  
Polymerase Chain Reaction Primers

In recent years, despite the significant improvement of sequencing technologies such as the pyrosequencing, rapid evaluation of microbial community structures remains very difficult because of the abundance and complexity of organisms in almost all natural microbial communities. In this paper, a group of phylum-specific primers were elaborately designed based on a single nucleotide discrimination technology to quantify the main microbial community structure from GuJingGong pit mud samples using the real-time quantitative PCR (qPCR). Specific PCR (polymerase chain reaction) primers targeting a particular group would provide promising sensitivity and more in-depth assessment of microbial communities.

scholarly journals Coupled changes in soil organic carbon fractions and microbial community composition in urban and suburban forests

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Xueying Zhang ◽  
Xiaomei Chen ◽  
Muying Liu ◽  
Zhanying Xu ◽  
Hui Wei
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Organic Carbon ◽  
Soil Organic Carbon ◽  
Community Composition ◽  
Microbial Community Structure ◽  
Soil Microorganisms ◽  
Microbial Community Composition ◽  
Soil C ◽  
Suburban Forests

Abstract Climate change and rapid urbanization have greatly impacted urban forest ecosystems and the carbon (C) cycle. To assess the effects of urbanization on forest soil C and soil microorganisms, six natural forests in a highly-urbanized region were selected as the research objects. Soil samples were collected to investigate the content and fractions of the soil organic carbon (SOC), as well as the soil microbial community composition. The results showed that the SOC content and fractions were substantially lower in the urban forests than in the suburban forests. Meanwhile, the total amount of phospholipid fatty acids (PLFAs) at suburban sites was twice more than that at urban sites, with shifts in microbial community structure. The potential differences in C inputs and nutrient limitation in urban forests may aggravate the low quantity and quality of SOC and consequently impact microbial community abundance and structure. Variation in microbial community structure was found to explain the loss of soil C pools by affecting the C inputs and promoting the decomposition of SOC. Therefore, the coupled changes in SOC and soil microorganisms induced by urbanization may adversely affect soil C sequestration in subtropical forests.

A quantitative comparison of microbial community structure of estuarine sediments from microcosms and the field

1986 ◽  
Vol 32 (4) ◽  
pp. 319-325 ◽  
Author(s):  
Thomas W. Federle ◽  
Robert J. Livingston ◽  
Loretta E. Wolfe ◽  
David C. White
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Ecological Factors ◽  
Estuarine Sediments ◽  
Physical Factors ◽  
Multivariate Statistical ◽  
Apalachicola Bay ◽  
Sound Experiment

Estuarine soft-bottom sediments in microcosms and the field were compared with regard to microbial community structure. Community structure was determined by analyzing the fatty acids derived from the microbial lipids in the sediments. Fatty acid profiles were compared using a multivariate statistical approach. Experiments were performed using sediments from St. George Sound and Apalachicola Bay, Florida. The community structure of St. George Sound sediments was apparently controlled by epibenthic predators. In Apalachicola Bay, the dominant influences were physical factors related to the flow of the Apalachicola River. In the St. George Sound experiment, microbial communities in the microcosms differed from those in the field after only 2 weeks, and the degree of this difference increased substantially as time progressed. In the Apalachicola Bay experiment, although microbial communities in the microcosms were detectably different from those in the field, the degree of this difference was not large nor did it increase with time. This differential behavior of sediment communities from different sites may be related to the different ecological factors regulating community composition at these sites.

scholarly journals Microbial community structure in the western tropical South Pacific

2018 ◽  
Vol 15 (12) ◽  
pp. 3909-3925 ◽  
Author(s):  
Nicholas Bock ◽  
France Van Wambeke ◽  
Moïra Dion ◽  
Solange Duhamel
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
N2 Fixation ◽  
Phytoplankton Biomass ◽  
South Pacific ◽  
Global Ocean ◽  
Bottom Up

Abstract. Oligotrophic regions play a central role in global biogeochemical cycles, with microbial communities in these areas representing an important term in global carbon budgets. While the general structure of microbial communities has been well documented in the global ocean, some remote regions such as the western tropical South Pacific (WTSP) remain fundamentally unexplored. Moreover, the biotic and abiotic factors constraining microbial abundances and distribution remain not well resolved. In this study, we quantified the spatial (vertical and horizontal) distribution of major microbial plankton groups along a transect through the WTSP during the austral summer of 2015, capturing important autotrophic and heterotrophic assemblages including cytometrically determined abundances of non-pigmented protists (also called flagellates). Using environmental parameters (e.g., nutrients and light availability) as well as statistical analyses, we estimated the role of bottom–up and top–down controls in constraining the structure of the WTSP microbial communities in biogeochemically distinct regions. At the most general level, we found a “typical tropical structure”, characterized by a shallow mixed layer, a clear deep chlorophyll maximum at all sampling sites, and a deep nitracline. Prochlorococcus was especially abundant along the transect, accounting for 68 ± 10.6 % of depth-integrated phytoplankton biomass. Despite their relatively low abundances, picophytoeukaryotes (PPE) accounted for up to 26 ± 11.6 % of depth-integrated phytoplankton biomass, while Synechococcus accounted for only 6 ± 6.9 %. Our results show that the microbial community structure of the WTSP is typical of highly stratified regions, and underline the significant contribution to total biomass by PPE populations. Strong relationships between N2 fixation rates and plankton abundances demonstrate the central role of N2 fixation in regulating ecosystem processes in the WTSP, while comparative analyses of abundance data suggest microbial community structure to be increasingly regulated by bottom–up processes under nutrient limitation, possibly in response to shifts in abundances of high nucleic acid bacteria (HNA).

scholarly journals Microbial community structure and the relationship with soil carbon and nitrogen in an original Korean pine forest of Changbai Mountain, China

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Minghui Liu ◽  
Xin Sui ◽  
Yanbo Hu ◽  
Fujuan Feng
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Organic Carbon ◽  
Microbial Community Structure ◽  
Soil Microbes ◽  
Mixed Forest ◽  
Korean Pine ◽  
Soil Microbial ◽  
The Relationship ◽  
Main Factor

Abstract Background The broad-leaved Korean pine mixed forest is an important and typical component of a global temperate forest. Soil microbes are the main driver of biogeochemical cycling in this forest ecosystem and have complex interactions with carbon (C) and nitrogen (N) components in the soil. Results We investigated the vertical soil microbial community structure in a primary Korean pine-broadleaved mixed forest in Changbai Mountain (from 699 to 1177 m) and analyzed the relationship between the microbial community and both C and N components in the soil. The results showed that the total phospholipid fatty acid (PLFA) of soil microbes and Gram-negative bacteria (G-), Gram-positive bacteria (G+), fungi (F), arbuscular mycorrhizal fungi (AMF), and Actinomycetes varied significantly (p < 0.05) at different sites (elevations). The ratio of fungal PLFAs to bacterial PLFAs (F/B) was higher at site H1, and H2. The relationship between microbial community composition and geographic distance did not show a distance-decay pattern. The coefficients of variation for bacteria were maximum among different sites (elevations). Total soil organic carbon (TOC), total nitrogen (TN), soil water content (W), and the ratio of breast-height basal area of coniferous trees to that of broad-leaved tree species (RBA) were the main contributors to the variation observed in each subgroup of microbial PLFAs. The structure equation model showed that TOC had a significant direct effect on bacterial biomass and an indirect effect upon bacterial and fungal biomass via soil readily oxidized organic carbon (ROC). No significant relationship was observed between soil N fraction and the biomass of fungi and bacteria. Conclusion The total PLFAs (tPLFA) and PLFAs of soil microbes, including G-, G+, F, AMF, and Actinomycetes, were significantly affected by elevation. Bacteria were more sensitive to changes in elevation than other microbes. Environmental heterogeneity was the main factor affecting the geographical distribution pattern of microbial community structure. TOC, TN, W and RBA were the main driving factors for the change in soil microbial biomass. C fraction was the main factor affecting the biomass of fungi and bacteria and ROC was one of the main sources of the microbial-derived C pool.

Land use change in Amazonian Dark Earth and Acrisol: Responses of organic carbon, organic matter composition and microbial carbon utilisation

2020 ◽  
Author(s):  
Klaus Jarosch ◽  
Luis Carlos Colocho Hurtarte ◽  
Konstantin Gavazov ◽  
Aleksander Westphal Muniz ◽  
Christoph Müller ◽  
...  
Keyword(s):  
Land Use ◽  
Organic Matter ◽  
Community Structure ◽  
Microbial Community ◽  
Organic Carbon ◽  
Land Use Change ◽  
Microbial Community Structure ◽  
Secondary Forest ◽  
Soil Types ◽  
Amazonian Dark Earth

&lt;p&gt;The conversion of tropical forest for cassava cultivation is widely known to decrease the soil organic matter (OM) and nutrient contents of highly weathered soils in the tropics. Amazonian Dark Earth (ADE) might be affected less due to their historical anthropogenic amelioration with e.g. charcoal, ceramics and bones, leading to higher soil OM and nutrient concentrations. In this study, we analysed the effect of land use change on the OM dynamics and its composition under tropical conditions, using ADE and an adjacent Acrisol (ACR) as model systems. Soil samples were obtained south of Manaus (Brazil), from a secondary forest and an adjacently located 40-year-old cassava plantation. The land use change induced a severe decrease of organic carbon (OC) concentrations in ADE (from 35 to 15&amp;#160;g&amp;#160;OC&amp;#160;kg&lt;sup&gt;&amp;#8209;1&lt;/sup&gt;) while OC in the adjacent ACR was less affected (18 to 16&amp;#160;g&amp;#160;OC&amp;#160;kg&lt;sup&gt;&amp;#8209;1&lt;/sup&gt;). Soils were analysed by &lt;sup&gt;13&lt;/sup&gt;C NMR spectroscopy to obtain information on how the conversion of secondary forest to cassava affected the chemical composition of OM. Our results show that land use change induces differences in the OM composition: The OM in ADE changes to a more decomposed state (increase of alkyl:O/N-alkyl ratio) whereas the OM in ACR changes to a less decomposed state (decrease of alkyl:O/N-alkyl ratio). According to a molecular mixing model, land use change influenced mostly the proportion of lipids, which might be related with a change of the plant input. The incubation of the soils with &lt;sup&gt;13&lt;/sup&gt;C glucose enabled resolving how soil microorganisms were affected by land use change. In both soil types ADE and ACR, land use change caused a reduction of the total &lt;sup&gt;13&lt;/sup&gt;C glucose respiration by approximately one third in a 7-days incubation, implying lower microbial activity. Microorganisms in both soil types appear to be more readily active in soils under forest, since we observed a distinct lag time between &lt;sup&gt;13&lt;/sup&gt;C glucose addition and respiration under cassava planation. This indicated differences in microbial community structure, which we will assess further by determining the &lt;sup&gt;13&lt;/sup&gt;C label uptake by the microbial biomass and the microbial community structure using &lt;sup&gt;13&lt;/sup&gt;C PLFA analysis. Preliminary results from synchrotron-based STXM demonstrate a distinct arrangement of OM at fine-sized charcoal-particle interfaces. Samples of soils receiving &lt;sup&gt;13&lt;/sup&gt;C label will be further analysed by NanoSIMS with the hypothesis that charcoal interfaces foster nutrient dynamics at the microscale. Despite the high loss of OC in the ameliorated ADE through land use change, the remaining OM might improve the nutrient availability thanks to charcoal interactions compared to the ACR. Our results contribute to a better understanding of the sensitivity of OM upon land use change and how the microbial community is responding to land use change in highly weathered tropical soils.&lt;/p&gt;

Spatial variation in microbial community structure, richness, and diversity in an alluvial aquifer

2012 ◽  
Vol 58 (9) ◽  
pp. 1135-1151 ◽  
Author(s):  
P.G. Medihala ◽  
J.R. Lawrence ◽  
G.D.W. Swerhone ◽  
D.R. Korber
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Spatial Variability ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Microbial Community Composition ◽  
Alluvial Aquifer ◽  
Gradient Gel Electrophoresis

Relatively little is known regarding the spatial variability of microbial communities in aquifers where well fouling is an issue. In this study 2 water wells were installed in an alluvial aquifer located adjacent to the North Saskatchewan River and an associated piezometer network developed to facilitate the study of microbial community structure, richness, and diversity. Carbon utilization data analysis revealed reduced microbial activity in waters collected close to the wells. Functional PCR and quantitative PCR analysis indicated spatial variability in the potential for iron-, sulphate-, and nitrate-reducing activity at all locations in the aquifer. Denaturing gradient gel electrophoresis analysis of aquifer water samples using principal components analyses indicated that the microbial community composition was spatially variable, and denaturing gradient gel electrophoresis sequence analysis revealed that bacteria belonging to the genera Acidovorax , Rhodobacter , and Sulfuricurvum were common throughout the aquifer. Shannon’s richness (H′) and Pielou’s evenness (J′) indices revealed a varied microbial diversity (H′ = 1.488–2.274) and an even distribution of microbial communities within the aquifer (J′ = 0.811–0.917). Overall, these analyses revealed that the aquifer’s microbial community varied spatially in terms of composition, richness, and metabolic activity. Such information may facilitate the diagnosis, prevention, and management of fouling.

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