Soil Microbial Community Structure and Physicochemical Properties in Amomum tsaoko-based Agroforestry Systems in the Gaoligong Mountains, Southwest China

Amomum tsaoko is cultivated in forests of tropical and subtropical regions of China, and the planting area is expanding gradually. However, little attention has been paid to the impact of A. tsaoko cultivation on the soil characteristics of the regions. We analyzed the effects of the A. tsaoko-forest agroforestry system (AFs) on the composition of soil microbial communities with increasing stand ages. We also compared the soil physicochemical properties, microbial biomass, and phospholipid fatty acid (PLFA) composition between native forest (NF) and AFs. The results showed that the level of total carbon, nitrogen, and organic matter dramatically dropped in AFs with increasing stand ages. pH affected other soil properties and showed close correlation to total carbon (P = 0.0057), total nitrogen (P = 0.0146), organic matter (P = 0.0075), hydrolyzable nitrogen (P = 0.0085), available phosphorus (P < 0.0001), and available potassium (P = 0.0031). PLFAs of bacteria (F = 4.650, P = 0.037), gram-positive bacteria (F = 6.640, P = 0.015), anaerobe (F = 5.672, P = 0.022), and total PLFA (F = 4.349, P = 0.043) were significantly affected by different treatments, with the greatest value for NF treatment, and least value for AF5. However, the microbial biomass declined during the initial 5 years of cultivation, but it reached the previous level after more than 10 years of cultivation. Our research suggests that AFs is a profitable land-use practice in the Gaoligong Mountains and that AFs showed a recovering trend of the soil nutrient condition with increasing stand ages. However, the severe loss of nitrogen in the soil of AFs requires additional nitrogen during cultivation to restore it to pre-cultivation levels.

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Soil microbial biomass—Interpretation and consideration for soil monitoring

Soil Research ◽

10.1071/sr10203 ◽

2011 ◽

Vol 49 (4) ◽

pp. 287 ◽

Cited By ~ 52

Author(s):

V. Gonzalez-Quiñones ◽

E. A. Stockdale ◽

N. C. Banning ◽

F. C. Hoyle ◽

Y. Sawada ◽

...

Keyword(s):

Organic Matter ◽

Microbial Biomass ◽

Soil Microorganisms ◽

Soil Microbial Biomass ◽

Biological Function ◽

Anthropogenic Change ◽

Soil Monitoring ◽

Soil Microbial ◽

Quality Assessments ◽

The Impact

Since 1970, measurement of the soil microbial biomass (SMB) has been widely adopted as a relatively simple means of assessing the impact of environmental and anthropogenic change on soil microorganisms. The SMB is living and dynamic, and its activity is responsible for the regulation of organic matter transformations and associated energy and nutrient cycling in soil. At a gross level, an increase in SMB is considered beneficial, while a decline in SMB may be considered detrimental if this leads to a decline in biological function. However, absolute SMB values are more difficult to interpret. Target or reference values of SMB are needed for soil quality assessments and to allow ameliorative action to be taken at an appropriate time. However, critical values have not yet been successfully identified for SMB. This paper provides a conceptual framework which outlines how SMB values could be interpreted and measured, with examples provided within an Australian context.

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Ester Linked Fatty Acid (ELFA) method should be used with caution for interpretating soil microbial communities and their relationships with environmental variables in forest soils

PLoS ONE ◽

10.1371/journal.pone.0251501 ◽

2021 ◽

Vol 16 (5) ◽

pp. e0251501

Author(s):

Wenjuan Yu ◽

Huanhuan Gao ◽

Hongzhang Kang

Keyword(s):

Fatty Acid ◽

Microbial Biomass ◽

Microbial Communities ◽

Forest Soils ◽

Environmental Variables ◽

Phospholipid Fatty Acid ◽

Soil Microbial Communities ◽

Environmental Drivers ◽

Soil Microbial ◽

Forest Sites

As an alternative for phospholipid fatty acid (PLFA) analysis, a simpler ester linked fatty acid (ELFA) analysis has been developed to characterize soil microbial communities. However, few studies have compared the two methods in forest soils where the contribution of nonmicrobial sources may be larger than that of microbial sources. Moreover, it remains unclear whether the two methods yield similar relationships of microbial biomass and composition with environmental variables. Here, we compared PLFA and ELFA methods with respect to microbial biomass and composition and their relationships with environmental variables in six oriental oak (Quercus variabilis) forest sites along a 1500-km latitudinal gradient in East China. We found that both methods had a low sample-to-sample variability and successfully separated overall community composition of sites. However, total, bacterial, and fungal biomass, the fungal-to-bacterial ratio, and the gram-positive to gram-negative bacteria ratio were not significantly or strongly correlated between the two methods. The relationships of these microbial properties with environmental variables (pH, precipitation, and clay) greatly differed between the two methods. Our study indicates that despite its simplicity, the ELFA method may not be as feasible as the PLFA method for investigating microbial biomass and composition and for identifying their dominant environmental drivers, at least in forest soils.

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Biogeographic Changes in Forest Soil Microbial Communities of Offshore Islands—A Case Study of Remote Islands in Taiwan

Forests ◽

10.3390/f12010004 ◽

2020 ◽

Vol 12 (1) ◽

pp. 4

Author(s):

Ed-Haun Chang ◽

Isheng Jason Tsai ◽

Shih-Hao Jien ◽

Guanglong Tian ◽

Chih-Yu Chiu

Keyword(s):

Organic Matter ◽

Soil Organic Matter ◽

Microbial Communities ◽

Phospholipid Fatty Acid ◽

Soil Microbial Communities ◽

Chemical Properties ◽

Principal Component ◽

Factors Affecting ◽

Soil Microbial

Biogeographic separation has been an important cause of faunal and floral distribution; however, little is known about the differences in soil microbial communities across islands. In this study, we determined the structure of soil microbial communities by analyzing phospholipid fatty acid (PLFA) profiles and comparing enzymatic activities as well as soil physio-chemical properties across five subtropical granite-derived and two tropical volcanic (andesite-derived) islands in Taiwan. Among these islands, soil organic matter, pH, urease, and PLFA biomass were higher in the tropical andesite-derived than subtropical granite-derived islands. Principal component analysis of PLFAs separated these islands into three groups. The activities of soil enzymes such as phosphatase, β-glucosidase, and β-glucosaminidase were positively correlated with soil organic matter and total nitrogen. Redundancy analysis of microbial communities and environmental factors showed that soil parent materials and the climatic difference are critical factors affecting soil organic matter and pH, and consequently the microbial community structure.

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Soil microbial communities following bush removal in a Namibian savanna

SOIL Discussions ◽

10.5194/soild-2-1393-2015 ◽

2015 ◽

Vol 2 (2) ◽

pp. 1393-1418

Author(s):

J. S. Buyer ◽

A. Schmidt-Küntzel ◽

M. Nghikembua ◽

J. E. Maul ◽

L. Marker

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Biomass ◽

Microbial Communities ◽

Microbial Community Structure ◽

Phospholipid Fatty Acid ◽

Soil Microbial Communities ◽

Management Approach ◽

Polymorphism Analysis ◽

Soil Microbial

Abstract. Savanna ecosystems are subject to desertification and bush encroachment, which reduce the carrying capacity for wildlife and livestock. Bush thinning is a management approach that can, at least temporarily, restore grasslands and raise the grazing value of the land. In this study we examined the soil microbial communities under bush and grass in Namibia. We analyzed the soil through a chronosequence where bush was thinned at 9, 5, or 3 years before sampling. Soil microbial biomass, the biomass of specific taxonomic groups, and overall microbial community structure was determined by phospholipid fatty acid analysis, while the community structure of Bacteria, Archaea, and fungi was determined by multiplex terminal restriction fragment length polymorphism analysis. Soil under bush had higher pH, C, N, and microbial biomass than under grass, and the microbial community structure was also altered under bush compared to grass. A major disturbance to the ecosystem, bush thinning, resulted in an altered microbial community structure compared to control plots, but the magnitude of this perturbation gradually declined with time. Community structure was primarily driven by pH, C, and N, while vegetation type, bush thinning, and time since bush thinning were of secondary importance.

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Arbuscular mycorrhiza enhance the rate of litter decomposition while inhibiting soil microbial community development

Scientific Reports ◽

10.1038/srep42184 ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 17

Author(s):

Heng Gui ◽

Kevin Hyde ◽

Jianchu Xu ◽

Peter Mortimer

Keyword(s):

Microbial Biomass ◽

Litter Decomposition ◽

Mycorrhizal Fungi ◽

Phospholipid Fatty Acid ◽

Soil Microbial Communities ◽

Arbuscular Mycorrhizal ◽

Fatty Acid Analysis ◽

Available N ◽

Soil Microbial ◽

Total Plfa

Abstract Although there is a growing amount of evidence that arbuscular mycorrhizal fungi (AMF) influence the decomposition process, the extent of their involvement remains unclear. Therefore, given this knowledge gap, our aim was to test how AMF influence the soil decomposer communities. Dual compartment microcosms, where AMF (Glomus mosseae) were either allowed access (AM+) to or excluded (AM−) from forest soil compartments containing litterbags (leaf litter from Calophyllum polyanthum) were used. The experiment ran for six months, with destructive harvests at 0, 90, 120, 150, and 180 days. For each harvest we measured AMF colonization, soil nutrients, litter mass loss, and microbial biomass (using phospholipid fatty acid analysis (PLFA)). AMF significantly enhanced litter decomposition in the first 5 months, whilst delaying the development of total microbial biomass (represented by total PLFA) from T150 to T180. A significant decline in soil available N was observed through the course of the experiment for both treatments. This study shows that AMF have the capacity to interact with soil microbial communities and inhibit the development of fungal and bacterial groups in the soil at the later stage of the litter decomposition (180 days), whilst enhancing the rates of decomposition.

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Soil microbial communities following bush removal in a Namibian savanna

SOIL ◽

10.5194/soil-2-101-2016 ◽

2016 ◽

Vol 2 (1) ◽

pp. 101-110 ◽

Cited By ~ 12

Author(s):

Jeffrey S. Buyer ◽

Anne Schmidt-Küntzel ◽

Matti Nghikembua ◽

Jude E. Maul ◽

Laurie Marker

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Biomass ◽

Microbial Communities ◽

Microbial Community Structure ◽

Phospholipid Fatty Acid ◽

Soil Microbial Communities ◽

Management Approach ◽

Polymorphism Analysis ◽

Soil Microbial

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Effects of land conversion on soil microbial community structure and diversity

10.21203/rs.3.rs-33038/v2 ◽

2020 ◽

Author(s):

Tong Zhang ◽

Yufei Liu ◽

xin Sui ◽

fuqiang Song

Keyword(s):

Land Use ◽

Community Structure ◽

Microbial Community ◽

Microbial Communities ◽

Soil Bacteria ◽

Soil Microbial Communities ◽

Forest Land ◽

Soil Microbial Community Structure ◽

Soil Microbial ◽

The Impact

Abstract Background : To study the impact of land-use change on soil microbial community structure and diversity in Northeast China, three typical land-use types (plough, grassland, and forest), grassland change to forest land and grassland change to plough, in the Qiqihar region of Heilongjiang Province were taken as research objects. Methods : MiSeq high-throughput sequencing technology based on bacterial 16S rRNA and fungal ITS rRNA was used to study the above community structure of soil bacteria and fungi and to explore the relationship between soil bacteria and soil environmental factors. Results : The results showed that the dominant bacterial phyla changed from Actinobacteria to Acidobacteria , the dominant fungal phyla changed from Ascomycetes to Basidiomycetes , and the ECM functional group increased significantly after the grassland was completely changed to forest land. After the grassland was changed to plough, the dominant phyla changed from Actinomycetes to Proteobacteria . The functional groups of pathogens and parasites increased significantly. There was no significant difference in the diversity of soil bacterial communities, and the diversity of fungal communities increased significantly. CCA showed that pH, MC, NO 3 - -N, TP and AP of soil were important factors affecting the composition of soil microbial communities, and changes in land-use patterns changed the physical and chemical properties of soils, thereby affecting the structure and diversity of microbial communities. Conclusions : Our research results clarify the impact of changes in land use on the characteristics of soil microbial communities and provide basic data on the healthy use of land.

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Impact of Fumigants on Soil Microbial Communities

Applied and Environmental Microbiology ◽

10.1128/aem.67.7.3245-3257.2001 ◽

2001 ◽

Vol 67 (7) ◽

pp. 3245-3257 ◽

Cited By ~ 169

Author(s):

A. Mark Ibekwe ◽

Sharon K. Papiernik ◽

Jianying Gan ◽

Scott R. Yates ◽

Ching-Hong Yang ◽

...

Keyword(s):

Microbial Communities ◽

Denaturing Gradient Gel Electrophoresis ◽

Phospholipid Fatty Acid ◽

Soil Microbial Communities ◽

Bacterial Biomass ◽

Effective Control ◽

Soil Microbial Community Structure ◽

Soil Dna ◽

Soil Microbial ◽

Plfa Analysis

ABSTRACT Agricultural soils are typically fumigated to provide effective control of nematodes, soilborne pathogens, and weeds in preparation for planting of high-value cash crops. The ability of soil microbial communities to recover after treatment with fumigants was examined using culture-dependent (Biolog) and culture-independent (phospholipid fatty acid [PLFA] analysis and denaturing gradient gel electrophoresis [DGGE] of 16S ribosomal DNA [rDNA] fragments amplified directly from soil DNA) approaches. Changes in soil microbial community structure were examined in a microcosm experiment following the application of methyl bromide (MeBr), methyl isothiocyanate, 1,3-dichloropropene (1,3-D), and chloropicrin. Variations among Biolog fingerprints showed that the effect of MeBr on heterotrophic microbial activities was most severe in the first week and that thereafter the effects of MeBr and the other fumigants were expressed at much lower levels. The results of PLFA analysis demonstrated a community shift in all treatments to a community dominated by gram-positive bacterial biomass. Different 16S rDNA profiles from fumigated soils were quantified by analyzing the DGGE band patterns. The Shannon-Weaver index of diversity,H, was calculated for each fumigated soil sample. High diversity indices were maintained between the control soil and the fumigant-treated soils, except for MeBr (H decreased from 1.14 to 0.13). After 12 weeks of incubation, Hincreased to 0.73 in the MeBr-treated samples. Sequence analysis of clones generated from unique bands showed the presence of taxonomically unique clones that had emerged from the MeBr-treated samples and were dominated by clones closely related to Bacillus spp. andHeliothrix oregonensis. Variations in the data were much higher in the Biolog assay than in the PLFA and DGGE assays, suggesting a high sensitivity of PLFA analysis and DGGE in monitoring the effects of fumigants on soil community composition and structure. Our results indicate that MeBr has the greatest impact on soil microbial communities and that 1,3-D has the least impact.

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Variation in soil microbial communities across a boreal spruce forest landscape

Canadian Journal of Forest Research ◽

10.1139/x07-232 ◽

2008 ◽

Vol 38 (6) ◽

pp. 1504-1516 ◽

Cited By ~ 17

Author(s):

Lisbet Holm Bach ◽

Åsa Frostegård ◽

Mikael Ohlson

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

Environmental Variables ◽

Phospholipid Fatty Acid ◽

Soil Microbial Communities ◽

Forest Landscape ◽

Spruce Forest ◽

Soil Microbial Community Structure ◽

Soil Microbial

We investigated soil microbial community structure by phospholipid fatty acid (PLFA) analysis in a mature boreal spruce forest landscape in southern Norway, with low diversity of vascular plants. We investigated the spatial variation in PLFAs and the importance of environmental variables in 10 plots (each 13 samples) in a study area of 1 km × 1 km. The scales investigated were 15 cm to 10 m within study plots and 100 m to 1 km between study plots. Soil microbial biomass varied 10-fold and we found a large variation in microbial community structure, even at distances of 15 cm. Samples aggregated into plots when PLFAs were subjected to a principal components analysis. Plot identity explained 36.3% of the variation in the PLFAs and geostatistical analysis showed that the microbial community structure displayed spatial dependence at within-plot distances. Environmental variables differed significantly between all plots but explained only minor parts of the variation in the overall PLFA pattern. The vegetation variables were, however, the best at explaining the PLFA pattern, and up to 60% of within-plot variation in individual plots, respectively, could be explained by vegetation variables, pH, and soil depth.

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Interaction between the Microbial Community and Invading Escherichia coli O157:H7 in Soils from Vegetable Fields

Applied and Environmental Microbiology ◽

10.1128/aem.03046-13 ◽

2013 ◽

Vol 80 (1) ◽

pp. 70-76 ◽

Cited By ~ 24

Author(s):

Zhiyuan Yao ◽

Haizhen Wang ◽

Laosheng Wu ◽

Jianjun Wu ◽

Philip C. Brookes ◽

...

Keyword(s):

Escherichia Coli ◽

Microbial Community ◽

Soil Microbial Community ◽

Phospholipid Fatty Acid ◽

Soil Microbial Communities ◽

Principal Component ◽

Content Type ◽

E Coli ◽

Soil Microbial ◽

The Impact

ABSTRACTThe survival ofEscherichia coliO157:H7 in soils can contaminate vegetables, fruits, drinking water, etc. However, data on the impact ofE. coliO157:H7 on soil microbial communities are limited. In this study, we monitored the changes in the indigenous microbial community by using the phospholipid fatty acid (PLFA) method to investigate the interaction of the soil microbial community withE. coliO157:H7 in soils. Simple correlation analysis showed that the survival ofE. coliO157:H7 in the test soils was negatively correlated with the ratio of Gram-negative (G−) to Gram-positive (G+) bacterial PLFAs (G−/G+ratio). In particular, levels of 14 PLFAs were negatively correlated with the survival time ofE. coliO157:H7. The contents of actinomycetous and fungal PLFAs in the test soils declined significantly (P, <0.05) after 25 days of incubation withE. coliO157:H7. The G−/G+ratio declined slightly, while the ratio of bacterial to fungal PLFAs (B/F ratio) and the ratio of normal saturated PLFAs to monounsaturated PLFAs (S/M ratio) increased, afterE. coliO157:H7 inoculation. Principal component analysis results further indicated that invasion byE. coliO157:H7 had some effects on the soil microbial community. Our data revealed that the toxicity ofE. coliO157:H7 presents not only in its pathogenicity but also in its effect on soil microecology. Hence, close attention should be paid to the survival ofE. coliO157:H7 and its potential for contaminating soils.

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