scholarly journals Soil Microbial Community Succession Based on PhoD and Gcd Genes along a Chronosequence of Sand-Fixation Forest

Forests ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1707
Author(s):  
Fei Wang ◽  
Ying Zhang ◽  
Yong Xia ◽  
Zhenbo Cui ◽  
Chengyou Cao
Keyword(s):  
Microbial Community ◽  
Soil Properties ◽  
Microbial Communities ◽  
Organic Phosphorus ◽  
Glucose Dehydrogenase ◽  
Sand Dunes ◽  
Illumina Miseq ◽  
N Fixation ◽  
Soil P ◽  
Plantation Development

Revegetation by planting shrubs on moving sand dunes is widely used to control desertification in arid/semi-arid areas. The soil including microbial community can gradually be improved along with plantation development. The purposes of this study were (1) to investigate the responses of microbial communities involved in the mineralization of soil organic phosphorus (OP) and dissolution of inorganic P (IOP) in the development of sand-fixating plantation and (2) to discuss the interactions between P turnover microbial communities and soil properties. We assessed the compositions of soil phoD gene (one of the Pho regulons encoding alkaline phosphomonoesterases) and gcd gene (encoding glucose dehydrogenase) in microbial community by using high-throughput Illumina MiSeq sequencing in a chronosequence of Caragana microphylla plantations (0-, 10-, 20-, and 37-year plantations and a native C. microphylla shrub forest) in Horqin Sandy Land, Northeast China. Soil properties including soil nutrients, enzymatic activity, and P fractions were also determined. The abundance of phoD and gcd genes linearly increased with the plantation age. However, the diversity of soil phoD microbes was more abundant than that of gcd. The phoD gene abundance and the fractions of total OP and IOP were positively correlated with the activity of phosphomonoesterase. Actinobacteria and Streptomycetaceae were the dominant phoD taxa, while Proteobacteria and Rhizobiaceae were the dominant gcd taxa. Plantation development facilitated the progressive successions of soil phoD and gcd communities resulting from the increase in the abundance of dominant taxa. Total soil N, NH4-N, and available K were the main factors affecting the structures of phoD and gcd communities, while pH was not significantly influencing factor in such arid and nutrient-poor sandy soil. Many phoD or gcd OTUs were classified into Rhizobium and Bradyrhizobium, suggesting the coupling relationship between soil P turnover and N fixation.

scholarly journals Successions of Soil phoD And gcd Microbial Communities Along a Chronosequence of Sand-Fixation Forest

2021 ◽  
Author(s):  
Fei Wang ◽  
Ying Zhang ◽  
Yong Xia ◽  
Zhenbo Cui ◽  
Chengyou Cao
Keyword(s):  
Soil Properties ◽  
Microbial Communities ◽  
Organic Phosphorus ◽  
Glucose Dehydrogenase ◽  
Sand Dunes ◽  
Illumina Miseq ◽  
N Fixation ◽  
Total N ◽  
Soil P ◽  
Plantation Development

Abstract Revegetation by planting shrubs on moving sand dunes is widely used to control desertification in arid/semi-arid areas. The soil microbial community can gradually recover along with plantation development. The purposes of this study were (1) to investigate the responses of microbial communities involved in the mineralization of soil organic phosphorus (OP) and dissolution of inorganic P (IOP) to the development of sand-fixation plantation and (2) to discuss the interactions between P turnover microbial communities and soil properties. We detected the diversities of soil phoD gene (one of the Pho regulons encoding alkaline phosphomonoesterases) and gcd gene (encoding glucose dehydrogenase) and the compositions of phoD and gcd communities by using the high-throughput Illumina MiSeq sequencing technique in a chronosequence of Caragana microphylla plantations (0-, 10-, 20-, and 37-year plantations and a native C. microphylla shrub forest) in Horqin Sandy Land, northeast China. Soil properties including soil nutrients, enzymatic activity, and P fractions were also determined. The abundance of phoD and gcd genes linearly increased with the plantation age. However, the diversity of soil phoD microbes was more abundant than that of gcd. The phoD gene abundance and the fractions of total OP and IOP were positively correlated with the activity of phosphomonoesterase. Actinobacteria and Streptomycetaceae were absolutely dominant phoD taxa, while Proteobacteria and Rhizobiaceae were absolutely dominant gcd taxa. Plantation development facilitated the progressive successions of soil phoD and gcd communities resulting from the asymmetric increase in the abundance of dominant taxa. Soil total N, NH4-N, and available K were the main factors affecting the structures of phoD and gcd communities, while pH was not the main influencing factor in such arid and nutrient-poor sandy soil. Many phoD or gcd operational taxonomic units were classified into Rhizobium and Bradyrhizobium, suggesting the coupling relationship between soil P turnover and N fixation.

scholarly journals Pollutant-Removing Biofilter Strains Associated with High Ammonia and Hydrogen Sulfide Removal Rate in a Livestock Wastewater Treatment Facility

2021 ◽  
Vol 13 (13) ◽  
pp. 7358
Author(s):  
Dong-Hyun Kim ◽  
Hyun-Sik Yun ◽  
Young-Saeng Kim ◽  
Jong-Guk Kim
Keyword(s):  
Wastewater Treatment ◽  
Hydrogen Sulfide ◽  
Microbial Community ◽  
Microbial Communities ◽  
Illumina Miseq ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
Treatment Facility ◽  
Livestock Wastewater ◽  
Wastewater Treatment Facility

This study analyzed the microbial community metagenomically to determine the cause of the functionality of a livestock wastewater treatment facility that can effectively remove pollutants, such as ammonia and hydrogen sulfide. Illumina MiSeq sequencing was used in analyzing the composition and structure of the microbial community, and the 16S rRNA gene was used. Through Illumina MiSeq sequencing, information such as diversity indicators as well as the composition and structure of microbial communities present in the livestock wastewater treatment facility were obtained, and differences between microbial communities present in the investigated samples were compared. The number of reads, operational taxonomic units, and species richness were lower in influent sample (NLF), where the wastewater enters, than in effluent sample (NL), in which treated wastewater is found. This difference was greater in June 2019 than in January 2020, and the removal rates of ammonia (86.93%) and hydrogen sulfide (99.72%) were also higher in June 2019. In both areas, the community composition was similar in January 2020, whereas the influent sample (NLF) and effluent sample (NL) areas in June 2019 were dominated by Proteobacteria (76.23%) and Firmicutes (67.13%), respectively. Oleiphilaceae (40.89%) and Thioalkalibacteraceae (12.91%), which are related to ammonia and hydrogen sulfide removal, respectively, were identified in influent sample (NLF) in June 2019. They were more abundant in June 2019 than in January 2020. Therefore, the functionality of the livestock wastewater treatment facility was affected by characteristics, including the composition of the microbial community. Compared to Illumina MiSeq sequencing, fewer species were isolated and identified in both areas using culture-based methods, suggesting Illumina MiSeq sequencing as a powerful tool to determine the relevance of microbial communities for pollutant removal.

Alleviating Continuous Monocropping Obstacle in Melon: Biological Elimination of Phenolic Acid

2020 ◽  
Author(s):  
Huiqin Xie ◽  
Yongli Ku ◽  
Xiangna Yang ◽  
Le Cao ◽  
Xueli Mei ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Phenolic Acids ◽  
Fruit Quality ◽  
High Performance ◽  
Soil Microbial Communities ◽  
Illumina Miseq ◽  
Continuous Cropping ◽  
Soil Microbial

Abstract Background: Melon (Cucumis melo L.) is one of the most important fruit crops grown in China. However, the yield and quality of melon have significantly declined under continuous cropping. Phenolic acids are believed to be associated with the continuous monocropping obstacle (CMO) and can influence plant microbe interactions. Coumaric acid (CA) is one of the major phenolic acids found in melon root exudates. The objectives of this study were to estimate the elimination of CA by the soil bacterium K3 as well as its effects on mitigating melon CMO. CA degradation was investigated by monitoring the CA retained in the growth medium using high performance liquid chromatography (HPLC). The effects of CA and K3 on rhizosphere soil microbial communities were investigated by the spread plate method and Illumina MiSeq sequencing. Furthermore, the effects of CA and K3 on melon seedling growth were measured under potted conditions. The changes in soil enzymes and fruit quality under K3 amendment were examined in a greenhouse experiment. Result:The results suggest that the addition of CA had the same result as the CMO, such as deterioration of the microbial community and slower growth of melon plants. HPLC and microbial analysis showed that K3 had a pronounced ability to decompose CA and could improve the soil microbial community environment. Soil inoculation with K3 agent could significantly improve the fruit quality of melon.Conclusion: Our results show that the effects of K3 in the soil are reflected by changes in populations and diversity of soil microbes and suggest that deterioration of microbial communities in soil might be associated with the growth constraint of melon in continuous monoculture systems.

scholarly journals Influence of Aged Biochar Modified by Cd2+ on Soil Properties and Microbial Community

2020 ◽  
Vol 12 (12) ◽  
pp. 4868
Author(s):  
Kun Li ◽  
Guangcai Yin ◽  
Qiuyuan Xu ◽  
Junhua Yan ◽  
Zeng-Yei Hseu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Soil Properties ◽  
Microbial Communities ◽  
Physicochemical Characteristics ◽  
Sorption Process ◽  
Gram Negative Bacteria ◽  
Gram Positive ◽  
Gram Negative ◽  
Gram Positive Bacteria ◽  
Cadmium Adsorption

Biochar is a promising addition for cadmium-contaminated soil in-situ remediation, but its surface properties change after aging, cadmium adsorption is not well-documented, and subsequent environmental effects are still unknown. In this study, wood-derived (Eucalyptus saligna Sm.) biochar was pre-treated to simulate aging and the cadmium sorption process. We then analyzed the resulting physicochemical characteristics. We conducted comparative incubation studies on three age stages of biochar under cadmium adsorption or no cadmium adsorption and then measured soil properties and microbial communities after incubation. Biochar addition raised soil organic carbon (SOC), and aging significantly increased C/N ratios. Aged biochar promoted higher microbial abundance. Aged biochar treatments possessed different microflora with more gram-positive bacteria, significantly altering gram-positive/gram-negative bacteria ratios. Aging significantly increased the oxygen-containing functional groups (OCFGs) and surface area (SA) of biochar. Thus, aged biochar adsorbed more cadmium. Cadmium-binding biochar increased the proportion of gram-negative bacteria and decreased the proportions of gram-positive bacteria and fungi. Similar patterns in phospholipid fatty acids (PLFAs) across adsorption treatments indicated that changes in microbial communities due to the effects of cadmium were confined. The results reveal that biochar aging altered microbial community structure and function more than cadmium binding.

Land use types influence soil microbial community through effects on soil properties in the dry-hot valley region in southwestern China

2021 ◽  
Author(s):  
Taicong Liu ◽  
Li Rong ◽  
Xingwu Duan ◽  
Zhe Chen
Keyword(s):  
Land Use ◽  
Microbial Community ◽  
Soil Properties ◽  
Microbial Communities ◽  
Indirect Effects ◽  
Structural Equation ◽  
Equation Model ◽  
Land Uses ◽  
Bacterial Composition ◽  
Soil Microbial

<p><strong>Abstract</strong>: Land use is one of the most important forms in agricultural production. Non-appropriate land use can cause deterioration of physical, chemical and biological properties of soil, thus affecting sustainable agriculture. Earlier reports showed that land use drastically altered microbial community composition. However, the mechanism of land use on microbial communities is still not fully understood. In the present study, we focus on the dry hot valley, characterized by high temperature and low humility, to test whether soil properties from four primary land uses including the land conversion from farmland (SLC), sugarcane land (SL), maize land with conventional tillage (CT) and bare land (BL) have different influences on soil microbial communities. The results showed that land uses altered bacterial and fungal community composition. In SL and BL, we found the respective absence of a kind of fungi at phylum the level. The abundances of several bacterial phyla in SL such as Gemmatimonadets and Acidobacteria associated with promoting mineralization were higher than that in other land uses. RDA indicated that bacterial communities were influenced by soil total nitrogen, total organic carbon and available potassium contents, and fungal communities were dominated by available potassium contents. SEM (structural equation model) showed that land use has direct and indirect effects on bacterial composition, while only indirect effects on fungal by land use. Land use indirectly affected bacterial composition through effects on soil moisture, clay and available potassium contents, whereas through effects on clay and available potassium for fungal composition. Land use exhibited greater impacts on bacterial composition than fungal composition, implying bacteria was more sensitive to land use changes compared to fungi in the dry-hot valley. Considering the low level of total potassium in soil under SL and CT, elevated potassium fertilizer would be a beneficial pathway to improve soil microbial composition and soil nutrients in the dry hot valley.</p><p><strong>Key word</strong>: Land use, Soil microbial community, Dry-hot valley, Soil properties, Structural equation model.</p>

scholarly journals Soil microbial community composition in a paddy field with different fertilization managements

2021 ◽  
pp. 1-11
Author(s):  
Limin Wang ◽  
Dongfeng Huang
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Soil Properties ◽  
Microbial Communities ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Alpha Diversity ◽  
Phosphorus Fertilization ◽  
Bacterial Phyla ◽  
P Fertilizer

Microbes play vital roles in soil quality; however, their response to N (nitrogen) and P (phosphorus) fertilization in acidic paddy soils of subtropical China remains poorly understood. Here, a 10-year field experiment was conducted to evaluate the effects of different fertilization treatments on microbial communities by Illumina MiSeq sequencing. The results showed that different fertilization treatments did not exert a significant effect on microbial alpha diversity, but altered soil properties, and thus affected microbial community composition. The microbial communities in the T1 (optimized N and P fertilizer) and T2 (excessive N fertilizer) treated soils differed from those in the T0 (no N and P fertilizer) and T3 (excessive P fertilizer) treated soils. In addition, the bacterial phyla Proteobacteria, Chloroflexi, and Acidobacteria, and the fungal phyla Ascomycota and Basidiomycota dominated all the fertilized treatments. Soil total potassium (TK) concentration was the most important factor driving the variation in bacterial community structure under different fertilization regimes, while the major factors shaping fungal community structure were soil TN and NO3–-N (nitrate N). These findings indicate that optimization of N and P application rates might result in variations in soil properties, which changed the microbial community structure in the present study.

scholarly journals Evidence of sustainable land use: the reclamation of desertified lands to plant vineyards

2021 ◽  
Author(s):  
Liang Zhang ◽  
Tingting Xue ◽  
Feifei Gao ◽  
Lin Yuan ◽  
Zhilei Wang ◽  
...  
Keyword(s):  
Land Use ◽  
Microbial Community ◽  
Soil Properties ◽  
Microbial Communities ◽  
Land Reclamation ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Sustainable Land Use ◽  
Available Nitrogen ◽  
Land Use Types

Desertified land reclamation for the purposes of winegrape cultivation can profoundly alter the properties of the underlying soil and the microbial communities therein. Herein, we assessed the effects of such reclamation of non-productive desert land on the soil microbial communities associated with the resultant vineyards, and to identify key soil properties related to these changes. Soil was collected from natural desert land (DL) and from different reclaimed vineyard types: Cabernet Sauvignon (CS), Merlot (M), Chardonnay (C), and Italian Riesling (IR). High-throughput sequencing was used to assess microbial community composition and diversity in these samples. Significant differences in soil organic carbon (SOC), total nitrogen, available nitrogen, available phosphorus, and pH were detected when comparing soil from DL and reclaimed lands. CS, M, C, and IR soils exhibited higher relative Actinobacteria, Proteobacteria, and Ascomycota abundance, while DL soil exhibited higher relative Acidobacteria and Mortierellomycota abundance. In total, 165 and 55 bacterial and fungal amplicon sequence variants or operational taxonomic units (ASVs/OTUs) were shared across land use types. Following reclamation, soil bacteria ASVs/OTUs in CS, M, C, and IR soils rose to 2846, 3191, 7630, and 6373, respectively. Biomarkers of these different land use types were successfully identified via an LDA Effect Size (LEfSe) approach, while key soil properties including pH, SOC, and available nitrogen were found to be associated with these changes in microbial community structural composition following reclamation. As such, our data indicate that viticulture in desertified regions can enhance soil properties and microbial diversity, thereby supporting sustainable land use.

scholarly journals Identification and Profiling of Microbial Community from Industrial Sludge

2021 ◽  
Author(s):  
Pooja Sharma ◽  
Surendra Pratap Singh
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Paper Industry ◽  
Illumina Miseq ◽  
Taxonomic Diversity ◽  
Disposal Site ◽  
Industry Studies ◽  
Indigenous Microbial Community ◽  
Microbial Strains

Abstract This study aims to identify microbial communities and their taxonomical profiling basis of order, species, genus, family, and class at the level in the sludge of pulp and paper industry. Studies showed dominant phyla in 16S rDNA Illumina Miseq analysis inside sludge were Anaerolinea, Pseudomonas, Clostridia, Bacteriodia, Gammaproteobacteria, Spirochetia, Deltaproteobacteria, Spirochaetaceae, Prolixibacteraceae and some unknown microbial strains are also dominant. The results of metabarcoding of the V3-V4 16S rRNA regions acquired from paired-end Illumina MiSeq sequencing were used to analyze bacterial communities and structure. Microorganisms can produce a vast variety of secondary metabolites, all of which are playing a crucial in biogeochemical cycle processes. The present work demonstrates the potential approach to sludge treatment in the open environment via the naturally adapted microorganism, which could be an essential addition to the disposal site. In summary, these investigations indicate that the indigenous microbial community is an acceptable bioresource for remediation or detoxification following secondary treatment. This research aims at understanding the structure of microbial communities and their taxonomic diversity (%) in highly contaminated sludge to perform in-situ bioremediation.

A peek in the micro-sized world: a review of design principles, engineering tools, and applications of engineered microbial community

2020 ◽  
Vol 48 (2) ◽  
pp. 399-409
Author(s):  
Baizhen Gao ◽  
Rushant Sabnis ◽  
Tommaso Costantini ◽  
Robert Jinkerson ◽  
Qing Sun
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Environmental Remediation ◽  
Real Life ◽  
Design Principles ◽  
Microbial Interactions ◽  
Potential Applications ◽  
New Gene ◽  
Global Biogeochemical Cycles ◽  
Synthetic Microbial Communities

Microbial communities drive diverse processes that impact nearly everything on this planet, from global biogeochemical cycles to human health. Harnessing the power of these microorganisms could provide solutions to many of the challenges that face society. However, naturally occurring microbial communities are not optimized for anthropogenic use. An emerging area of research is focusing on engineering synthetic microbial communities to carry out predefined functions. Microbial community engineers are applying design principles like top-down and bottom-up approaches to create synthetic microbial communities having a myriad of real-life applications in health care, disease prevention, and environmental remediation. Multiple genetic engineering tools and delivery approaches can be used to ‘knock-in' new gene functions into microbial communities. A systematic study of the microbial interactions, community assembling principles, and engineering tools are necessary for us to understand the microbial community and to better utilize them. Continued analysis and effort are required to further the current and potential applications of synthetic microbial communities.

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