scholarly journals A Standardized Method for Estimating the Functional Diversity of Soil Bacterial Community by Biolog® EcoPlatesTM Assay—The Case Study of a Sustainable Olive Orchard

2019 ◽  
Vol 9 (19) ◽  
pp. 4035 ◽  
Author(s):  
Adriano Sofo ◽  
Patrizia Ricciuti
Keyword(s):  
Bacterial Community ◽  
Functional Diversity ◽  
Soil Bacterial Community ◽  
Step Method ◽  
Olive Orchard ◽  
Correct Definition ◽  
Standardized Method ◽  
Soil Bacterial ◽  
Sustainable Conservation

Biolog® EcoPlates™ (Biolog Inc., Hayward, CA, USA) were developed to analyse the functional diversity of bacterial communities by means of measuring their ability to oxidize carbon substrates. This technique has been successfully adopted for studying bacterial soil communities from different soil environments, polluted soils and soils subjected to various agronomic treatments. Unfortunately, Biolog® EcoPlates™ assay, especially working on soil, can be difficult to reproduce and hard to standardize due to the lack of detailed procedures and protocols. The main problems of this technique mainly regard soil preparation, bacterial inoculum densities and a correct definition of blank during the calculation of the diversity indices. On the basis of our previous research on agricultural soils, we here propose a standardized and accurate step-by-step method for estimating the functional diversity of a soil bacterial community by Biolog® EcoPlatesTM assay. A case study of soils sampled in a Mediterranean olive orchard managed accordingly to sustainable/conservation practices was reported for justifying the standardized method here used. The results of this methodological paper could be important for correctly evaluating and comparing the microbiological fertility of soils managed by sustainable/conservation or conventional/non-conservation systems.

scholarly journals Changes in soil bacterial community diversity following the removal of invasive feral pigs from a Hawaiian tropical montane wet forest

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Nathaniel H. Wehr ◽  
Kealohanuiopuna M. Kinney ◽  
Nhu H. Nguyen ◽  
Christian P. Giardina ◽  
Creighton M. Litton
Keyword(s):  
Bacterial Community ◽  
Functional Diversity ◽  
Phylogenetic Diversity ◽  
Soil Microbial Communities ◽  
Soil Bacterial Community ◽  
Community Diversity ◽  
Feral Pigs ◽  
Bacterial Community Diversity ◽  
Soil Bacterial ◽  
Functional And Phylogenetic Diversity

Abstract Nonnative, invasive feral pigs (Sus scrofa) modify habitats by disturbing soils and vegetation, which can alter biogeochemical processes. Soil microbial communities drive nutrient cycling and therefore also play important roles in shaping ecosystem structure and function, but the responses of soil microbes to nonnative ungulate removal remains poorly studied. We examined changes in the soil bacterial community over a ~25 year chronosequence of feral pig removal in tropical montane wet forests on the Island of Hawai’i. We extracted bacterial eDNA from soil samples collected inside and outside of ungulate exclosures along this chronosequence and sequenced the eDNA using the Illumina platform. We found that ungulate removal increased diversity of soil bacteria, with diversity scores positively correlated with time since removal. While functional and phylogenetic diversity were not significantly different between pig present and pig removed soils, soil bulk density, which decreases following the removal of feral pigs, was a useful predictor of dissimilarity among sites and correlated to changes in functional diversity. Additionally, increases in soil porosity, potassium, and calcium were correlated to increases in functional diversity. Finally, sites with greater mean annual temperatures were shown to have higher scores of both functional and phylogenetic diversity. As such, we conclude that feral pigs influence overall bacterial community diversity directly while influencing functional diversity indirectly through alterations to soil structure and nutrients. Comparatively, phylogenetic differences between communities are better explained by mean annual temperature as a climatic predictor of community dissimilarity.

scholarly journals Effects of novel bioorganic fertilizer application on soil enzymes and bacterial community in multi-site rice paddies in China

AMB Express ◽  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Zuren Li ◽  
Jincai Han ◽  
Haodong Bai ◽  
Di Peng ◽  
Lifeng Wang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Field Experiments ◽  
Chemical Properties ◽  
Soil Bacterial Community ◽  
General Function ◽  
Rice Paddies ◽  
Phylogenetic Groups ◽  
Total N ◽  
Bioorganic Fertilizer ◽  
Soil Bacterial

AbstractApplication of a novel bioorganic fertilizer (BIO) has been effectively used to inhibit weeds in rice paddies. To identify changes in soil bacterial community and enzymes in response to BIO treatments, field experiments were carried out in five major rice-growing areas in China. The dominant phylogenetic groups recorded included Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Acidobacteria. Anaeromyxobacter, Bacteroides, Bifidobacterium, Escherichia- Shigella, Geobacter and Haliangium were significantly different between BIO-treatment and untreated control and aided in general function (R), amino acid transport, metabolism (E) and transcription (K) clusters. The soil chemical properties and enzyme activities were less affected by BIO at these study sites. RDA analysis showed that soil bacterial community had a significant positive correlations among northern latitude, eastern longitude, exchangeable K, total K, total P, soil pH, and total N, except for organic matter, hydrolytic N and extractable P. Overall, our work showed that application of BIO does not alter the main community structure and functional diversity of soil bacteria in rice paddies and should be encouraged for use as a sustainable weed management strategy.

scholarly journals Soil bacterial community in potato tuberosphere following repeated applications of a common scab suppressive antagonist

2021 ◽  
Vol 167 ◽  
pp. 104096
Author(s):  
Lea H. Hiltunen ◽  
Oili Tarvainen ◽  
Jani Kelloniemi ◽  
Jaakko Tanskanen ◽  
Jouni Karhu ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Common Scab ◽  
Soil Bacterial Community ◽  
Repeated Applications ◽  
Soil Bacterial

scholarly journals Effects of Simulated Nitrogen Deposition on the Bacterial Community of Urban Green Spaces

2021 ◽  
Vol 11 (3) ◽  
pp. 918
Author(s):  
Lingzi Mo ◽  
Augusto Zanella ◽  
Xiaohua Chen ◽  
Bin Peng ◽  
Jiahui Lin ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Negative Impact ◽  
Bacterial Community Composition ◽  
N Deposition ◽  
Soil Bacterial Community ◽  
Rrna Gene ◽  
Soil Dna ◽  
Urban Green ◽  
Soil Bacterial

Continuing nitrogen (N) deposition has a wide-ranging impact on terrestrial ecosystems. To test the hypothesis that, under N deposition, bacterial communities could suffer a negative impact, and in a relatively short timeframe, an experiment was carried out for a year in an urban area featuring a cover of Bermuda grass (Cynodon dactylon) and simulating environmental N deposition. NH4NO3 was added as external N source, with four dosages (N0 = 0 kg N ha−2 y−1, N1 = 50 kg N ha−2 y−1, N2 = 100 kg N ha−2 y−1, N3 = 150 kg N ha−2 y−1). We analyzed the bacterial community composition after soil DNA extraction through the pyrosequencing of the 16S rRNA gene amplicons. N deposition resulted in soil bacterial community changes at a clear dosage-dependent rate. Soil bacterial diversity and evenness showed a clear trend of time-dependent decline under repeated N application. Ammonium nitrogen enrichment, either directly or in relation to pH decrease, resulted in the main environmental factor related to the shift of taxa proportions within the urban green space soil bacterial community and qualified as a putative important driver of bacterial diversity abatement. Such an impact on soil life induced by N deposition may pose a serious threat to urban soil ecosystem stability and surrounding areas.

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