scholarly journals Biodiversity management of organic orchard enhances both ecological and economic profitability

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2137 ◽  
Author(s):  
Jie Meng ◽  
Lijun Li ◽  
Haitao Liu ◽  
Yong Li ◽  
Caihong Li ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Microbial Biomass Carbon ◽  
Organic Matter Content ◽  
Economic Benefits ◽  
Apple Orchard ◽  
Chemical Pollution ◽  
Native Plant ◽  
Biodiversity Management ◽  
Health Maintenance ◽  
Bacterial Phyla

Organic farming has been regarded as an alternative solution for both agricultural sustainability and human health maintenance. Few researches have concentrated on the differences of biodiversity and eco-economic benefits between organic and conventional orchards. Organic management (OM) of orchards mainly includes taking advantage of natural enemies and beneficial weeds as well as soil organisms and controlling harmful pests. Here we conducted a three-year experiment on the effects of managing biodiversity in an organic apple orchard, using cattle manure to enrich soil biota, propagating native plant to suppress weeds and applying ecological pest management to control pests. The effect was assessed against the conventional management (CM) model. We found that OM enhanced soil organic carbon, total nitrogen, microbial biomass carbon and nitrogen. The 16S rDNA high-throughput sequencing results indicated that the dominant bacterial phyla of the top soil wereProteobacteriaandActinobacteria, and OM had richer bacteria diversity with a 7% higher Shannon’s index than the CM. In particular, the relative abundance of rhizobium in the OM was higher than that of the CM. For OM,Duchesnea indicawas an ideal ground-cover plant to control weeds through winning the niche competition and thus decreased weeds’ Simpson, Shannon–Wiener and Pielou index by 38.2%, 53.8% and 16.9% separately. The phototactic pests’ weight and scarab beetle’s population were effectively decreased by 35% and 86% respectively through long time control and prevention. OM had an average of 20 times more earthworms than CM, and the maximum density had reached 369 m−2(0–20 cm soil). The dominant earthworm species of the OM were detritivores which preferring soil with high organic matter content. Due to no synthetic chemicals being used, the OM produced much safer apple fruits which were sold at high prices. Economically, up to a 103% increase of output–input ratio had been achieved in the OM. Our study clearly demonstrated that biodiversity management without chemical pollution increased the biodiversity of beneficial organisms, reduced antagonists of the fruit tree, and enhanced economic benefits of the apple orchard.

scholarly journals Seasonal Variation Characteristics of Bacteria and Fungi in PM2.5 in Typical Basin Cities of Xi’an and Linfen, China

Atmosphere ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 809
Author(s):  
Sen Wang ◽  
Wanyu Liu ◽  
Jun Li ◽  
Haotian Sun ◽  
Yali Qian ◽  
...  
Keyword(s):  
Seasonal Variation ◽  
Relative Abundance ◽  
Pathogenic Bacteria ◽  
High Throughput Sequencing ◽  
Fine Particulate Matter ◽  
Ecological Functions ◽  
Factors Affecting ◽  
Bacterial Phyla ◽  
Variation Characteristics ◽  
Bacteria And Fungi

Microorganisms existing in airborne fine particulate matter (PM2.5) have key implications in biogeochemical cycling and human health. In this study, PM2.5 samples, collected in the typical basin cities of Xi’an and Linfen, China, were analyzed through high-throughput sequencing to understand microbial seasonal variation characteristics and ecological functions. For bacteria, the highest richness and diversity were identified in autumn. The bacterial phyla were dominated by Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. Metabolism was the most abundant pathway, with the highest relative abundance found in autumn. Pathogenic bacteria (Pseudomonas, Acinetobacter, Serratia, and Delftia) were positively correlated with most disease-related pathways. Besides, C cycling dominated in spring and summer, while N cycling dominated in autumn and winter. The relative abundance of S cycling was highest during winter in Linfen. For fungi, the highest richness was found in summer. Basidiomycota and Ascomycota mainly constituted the fungal phyla. Moreover, temperature (T) and sulfur dioxide (SO2) in Xi’an, and T, SO2, and nitrogen dioxide (NO2) in Linfen were the key factors affecting microbial community structures, which were associated with different pollution characteristics in Xi’an and Linfen. Overall, these results provide an important reference for the research into airborne microbial seasonal variations, along with their ecological functions and health impacts.

scholarly journals Gut Microbiome Changes in Captive Plateau Zokors (Eospalax baileyi)

2021 ◽  
Vol 17 ◽  
pp. 117693432199635
Author(s):  
Daoxin Liu ◽  
Pengfei Song ◽  
Jingyan Yan ◽  
Haijing Wang ◽  
Zhenyuan Cai ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
High Throughput Sequencing ◽  
Tibet Plateau ◽  
Rrna Gene ◽  
Diversity Analysis ◽  
Bacterial Phyla ◽  
In Captivity ◽  
Relative Abundances ◽  
Plateau Zokor

Wild-caught animals must cope with drastic lifestyle and dietary changes after being induced to captivity. How the gut microbiome structure of these animals will change in response receives increasing attention. The plateau zokor ( Eospalax baileyi), a typic subterranean rodent endemic to the Qinghai-Tibet plateau, spends almost the whole life underground and is well adapted to the environmental pressures of both plateau and underground. However, how the gut microbiome of the plateau zokor will change in response to captivity has not been reported to date. This study compared the microbial community structure and functions of 22 plateau zokors before (the WS group) and after being kept in captivity for 15 days (the LS group, fed on carrots) using the 16S rRNA gene via high-throughput sequencing technology. The results showed that the LS group retained 973 of the 977 operational taxonomic units (OTUs) in the WS group, and no new OTUs were found in the LS group. The dominant bacterial phyla were Bacteroides and Firmicutes in both groups. In alpha diversity analysis, the Shannon, Sobs, and ACE indexes of the LS group were significantly lower than those of the WS group. A remarkable difference ( P < 0.01) between groups was also detected in beta diversity analysis. The UPGMA clustering, NMDS, PCoA, and Anosim results all showed that the intergroup difference was significantly greater than the intragroup difference. And compared with the WS group, the intragroup difference of the gut microbiota in the LS group was much larger, which failed to support the assumption that similar diets should drive convergence of gut microbial communities. PICRUSt revealed that although some functional categories displayed significant differences between groups, the relative abundances of these categories were very close in both groups. Based on all the results, we conclude that as plateau zokors enter captivity for a short time, although the relative abundances of different gut microbiota categories shifted significantly, they can maintain almost all the OTUs and the functions of the gut microbiota in the wild. So, the use of wild-caught plateau zokors in gut microbial studies is acceptable if the time in captivity is short.

scholarly journals Microbiological and faunal soil attributes of coffee cultivation under different management systems in Brazil

2015 ◽  
Vol 75 (4) ◽  
pp. 894-905 ◽  
Author(s):  
D. R. Lammel ◽  
L. C. B. Azevedo ◽  
A. M. Paula ◽  
R. D. Armas ◽  
D. Baretta ◽  
...  
Keyword(s):  
Mycorrhizal Fungi ◽  
Microbial Biomass Carbon ◽  
Integrated Management ◽  
Organic Matter Content ◽  
Arbuscular Mycorrhizal ◽  
Tropical Soils ◽  
Matter Content ◽  
Management Systems ◽  
Southeastern Brazil ◽  
Biological Parameters

Abstract Brazil is the biggest coffee producer in the world and different plantation management systems have been applied to improve sustainability and soil quality. Little is known about the environmental effects of these different management systems, therefore, the goal of this study was to use soil biological parameters as indicators of changes. Soils from plantations in Southeastern Brazil with conventional (CC), organic (OC) and integrated management systems containing intercropping of Brachiaria decumbens (IB) or Arachis pintoi (IA) were sampled. Total organic carbon (TOC), microbial biomass carbon (MBC) and nitrogen (MBN), microbial activity (C-CO2), metabolic quotient (qCO2), the enzymes dehydrogenase, urease, acid phosphatase and arylsulphatase, arbuscular mycorrhizal fungi (AMF) colonization and number of spores and soil fauna were evaluated. The greatest difference between the management systems was seen in soil organic matter content. The largest quantity of TOC was found in the OC, and the smallest was found in IA. TOC content influenced soil biological parameters. The use of all combined attributes was necessary to distinguish the four systems. Each management presented distinct faunal structure, and the data obtained with the trap method was more reliable than the TSBF (Tropical Soils) method. A canonic correlation analysis showed that Isopoda was correlated with TOC and the most abundant order with OC. Isoptera was the most abundant faunal order in IA and correlated with MBC. Overall, OC had higher values for most of the biological measurements and higher populations of Oligochaeta and Isopoda, corroborating with the concept that the OC is a more sustainable system.

scholarly journals Wild specimens of sand fly phlebotomine Lutzomyia evansi, vector of leishmaniasis, show high abundance of Methylobacterium and natural carriage of Wolbachia and Cardinium types in the midgut microbiome

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Rafael J. Vivero ◽  
Marcela Villegas-Plazas ◽  
Gloria E. Cadavid-Restrepo ◽  
Claudia Ximena Moreno Herrera ◽  
Sandra I. Uribe ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput Sequencing ◽  
Sand Fly ◽  
Human Populations ◽  
Rrna Gene ◽  
Remarkable Feature ◽  
Core Microbiome ◽  
Bacterial Phyla ◽  
Wide Range

AbstractPhlebotomine sand flies are remarkable vectors of several etiologic agents (virus, bacterial, trypanosomatid Leishmania), posing a heavy health burden for human populations mainly located at developing countries. Their intestinal microbiota is involved in a wide range of biological and physiological processes, and could exclude or facilitate such transmission of pathogens. In this study, we investigated the Eubacterial microbiome from digestive tracts of Lu. evansi adults structure using 16S rRNA gene sequence amplicon high throughput sequencing (Illumina MiSeq) obtained from digestive tracts of Lu. evansi adults. The samples were collected at two locations with high incidence of the disease in humans: peri-urban and forest ecosystems from the department of Sucre, Colombia. 289,068 quality-filtered reads of V4 region of 16S rRNA gene were obtained and clustered into 1,762 operational taxonomic units (OTUs) with 97% similarity. Regarding eubacterial diversity, 14 bacterial phyla and 2 new candidate phyla were found to be consistently associated with the gut microbiome content. Proteobacteria, Firmicutes, and Bacteroidetes were the most abundant phyla in all the samples and the core microbiome was particularly dominated by Methylobacterium genus. Methylobacterium species, are known to have mutualistic relationships with some plants and are involved in shaping the microbial community in the phyllosphere. As a remarkable feature, OTUs classified as Wolbachia spp. were found abundant on peri-urban ecosystem samples, in adult male (OTUs n = 776) and unfed female (OTUs n = 324). Furthermore, our results provide evidence of OTUs classified as Cardinium endosymbiont in relative abundance, notably higher with respect to Wolbachia. The variation in insect gut microbiota may be determined by the environment as also for the type of feeding. Our findings increase the richness of the microbiota associated with Lu. evansi. In this study, OTUs of Methylobacterium found in Lu. evansi was higher in engorged females, suggesting that there are interactions between microbes from plant sources, blood nutrients and the parasites they transmit during the blood intake.

scholarly journals Intraspecific variability in root traits and edaphic conditions influence soil microbiomes across 12 switchgrass cultivars

2020 ◽  
Author(s):  
Tayler Chicoine Ulbrich ◽  
Maren Friesen ◽  
Sarah S Roley ◽  
Lisa K Tiemann ◽  
Sarah E Evans
Keyword(s):  
Microbial Biomass ◽  
Fungal Community ◽  
Panicum Virgatum ◽  
Microbial Biomass Carbon ◽  
Intraspecific Variability ◽  
Root Traits ◽  
Soil Microbiome ◽  
Soil Conditions ◽  
Bacterial Phyla ◽  
Environmental Responses

Microbial communities help plants access nutrients and tolerate stress. Some microbiomes are specific to plant genotypes and, therefore, may contribute to intraspecific differences in plant growth and be a promising target for plant breeding. Switchgrass (Panicum virgatum L.) is a potential bioenergy crop with broad variation in yields and environmental responses; recent studies suggest that associations with distinct microbiomes may contribute to variation in cultivar yields. We used a common garden experiment to investigate variation in 12 mature switchgrass cultivar soil microbiomes and, further, to examine how root traits and soil conditions influence microbiome structure. We found that average root diameter varied up to 33% among cultivars and that they associated with distinct soil microbiomes. Cultivar had a larger effect on the soil bacterial than fungal community, but both were strongly influenced by soil properties. Root traits had a weaker effect on microbiome structure, but root length contributed to variation in the fungal community. Unlike the soil communities, the root bacterial communities did not group by cultivar, based on a subset of samples. Microbial biomass carbon and nitrogen and the abundance of several dominant bacterial phyla varied between ecotypes, but overall the differences in soil microbiomes were greater among cultivars than between ecotypes. Our findings show that there is not one soil microbiome that applies to all switchgrass cultivars, or even to each ecotype. These subtle but significant differences in root traits, microbial biomass, and the abundance of certain soil bacteria could explain differences in cultivar yields and environmental responses.

scholarly journals Biocontrol of Aspergillus flavus in Ensiled Sorghum by Water Kefir Microorganisms

2019 ◽  
Vol 7 (8) ◽  
pp. 253 ◽  
Author(s):  
Gonda ◽  
Garmendia ◽  
Rufo ◽  
Peláez ◽  
Wisniewski ◽  
...  
Keyword(s):  
Aspergillus Flavus ◽  
High Throughput Sequencing ◽  
Management Practice ◽  
Bacterial Phyla ◽  
Mixed Inoculum ◽  
Sorghum Grains ◽  
Before And After ◽  
Relevant Role ◽  
Abundant Genus ◽  
Water Kefir

The capacity of microorganisms from water kefir (WK) to control Aspergillus flavus growth during the aerobic phase of ensiled sorghum grains was determined. Sorghum inoculated with A. flavus was treated with filter-sterilized and non-sterilized water kefir, ensiled, and incubated 7 days at 25 °C. A. flavus growth was quantified by qPCR after incubation. Mold growth was inhibited in the presence of water kefir while no inhibition was observed when filter-sterilized water kefir was applied, demonstrating the relevant role of the microorganisms in the kefir water in the biocontrol process. Fungal and bacterial diversity in treated sorghum mini-silos was analyzed by high-throughput sequencing. Firmicutes was the predominant bacterial phyla and Lactobacillus represented the most abundant genus, while Ascomycota was the predominant fungal phyla with Saccharomyces and Pichia as the major genera. Bacterial and yeast counts before and after incubation indicated that the microbial community obtained from WK was able to grow in the sorghum mini-silos in the presence of A. flavus. Results of the present work indicate that the use of a mixed inoculum of microorganisms present in WK may represent an alternative management practice to avoid the growth of A. flavus in ensiled sorghum grains and the concomitant contamination with aflatoxins.

scholarly journals High-Throughput, Sequence-Based Analysis of the Microbiota of Greek Kefir Grains from Two Geographic Regions

2020 ◽  
Vol 58 (2) ◽  
pp. 138-146
Author(s):  
Mary S. Kalamaki ◽  
Apostolos S. Angelidis
Keyword(s):  
Bacterial Community ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Geographic Origin ◽  
Probiotic Properties ◽  
Sequencing Analysis ◽  
Microbial Composition ◽  
Bacterial Phyla ◽  
Geographic Regions ◽  
Kefir Grains

Research background. Kefir is a natural probiotic drink traditionally produced by milk fermentation using kefir grains. Kefir grains are composed of a complex population of bacteria and yeasts embedded in a polysaccharide-protein matrix. The geographic origin of kefir grains may largely influence their microbial composition and the associated kefir drink properties. Although the detailed bacterial composition of kefir grains from several geographic regions has been reported, to date, analogous data about the microbiome of Greek kefir are lacking. Hence, the aim of this study is to investigate the structure and the diversity of the bacterial community of Greek kefir grains.Experimental approach. The bacterial community structure and diversity of two different kefir grains from distant geographic regions in Greece were examined via high-throughput sequencing analysis, a culture-independent metagenomic approach, targeting the 16S rRNA V4 variable region, in order to gain a deeper understanding of their bacterial population diversities.Results and conclusions. Firmicutes (a phylum that includes lactic acid bacteria) was strikingly dominant amongst the identified bacterial phyla, with over 99 % of the sequences from both kefir grains classified to this phylum. At the family level, Lactobacillaceae sequences accounted for more than 98 % of the operational taxonomic units (OTUs), followed by Ruminococcaceae, Lahnospiraceae, Bacteroidaceae and other bacterial families of lesser abundance. Α relatively small number of bacterial genera dominated, with Lactobacillus kefiranofaciens being the most abundant in both kefir grains (95.0 % of OTUs in kefir A and 96.3 % of OTUs in kefir B). However, a quite variable subdominant population was also present in both grains, including bacterial genera that have been previously associated with the gastrointestinal tract of humans and animals, some of which are believed to possess probiotic properties (Faecalibacterium spp., Bacteroides spp., Blautia spp.). Differences among the bacterial profiles of the two grains were very small indicating a high homogeneity despite the distant geographic origin.Novelty and scientific contribution. This is the first study to deeply explore and report on the bacterial diversity and species richness of Greek kefir.

scholarly journals Co-occurrence patterns in aquatic bacterial communities across changing permafrost landscapes

2015 ◽  
Vol 12 (13) ◽  
pp. 10233-10269 ◽  
Author(s):  
J. Comte ◽  
C. Lovejoy ◽  
S. Crevecoeur ◽  
W. F. Vincent
Keyword(s):  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Habitat Preferences ◽  
Keystone Species ◽  
Small World ◽  
Rrna Gene ◽  
Permafrost Degradation ◽  
Bacterial Phyla ◽  
Organic Carbon Concentration ◽  
Occurrence Patterns

Abstract. Permafrost thaw ponds and lakes are widespread across the northern landscape and may play a central role in global biogeochemical cycles, yet knowledge about their microbial ecology is limited. We sampled a set of thaw ponds and lakes as well as shallow rock-basin lakes that are located in distinct valleys along a North–South permafrost degradation gradient. We applied high-throughput sequencing of the 16S rRNA gene to determine co-occurrence patterns among bacterial taxa, and then analyzed these results relative to environmental variables to identify factors controlling bacterial community structure. Network analysis was applied to identify possible ecological linkages among the bacterial taxa and with abiotic and biotic variables. The results showed an overall high level of shared taxa among bacterial communities within each valley, however the bacterial co-occurrence patterns were non-random, with evidence of habitat preferences. There were taxonomic differences in bacterial assemblages among the different valleys that were statistically related to dissolved organic carbon concentration, conductivity and phytoplankton biomass. Co-occurrence networks revealed complex interdependencies within the bacterioplankton communities and showed contrasting linkages to environmental conditions among the main bacterial phyla. The thaw pond networks were composed of a limited number of highly connected taxa. This "small world network" property would render the communities more robust to environmental change but vulnerable to the loss of microbial keystone species.

scholarly journals Filtered mud improves sugarcane growth and modifies the functional abundance and structure of soil microbial populations

PeerJ ◽  
2022 ◽  
Vol 10 ◽  
pp. e12753
Author(s):  
Ahmad Yusuf Abubakar ◽  
Muhammed Mustapha Ibrahim ◽  
Caifang Zhang ◽  
Muhammad Tayyab ◽  
Nyumah Fallah ◽  
...  
Keyword(s):  
Nutrient Cycling ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Soil Nutrient ◽  
Clay Loam ◽  
Sugarcane Production ◽  
Bacterial Phyla ◽  
Soil Microbial ◽  
Soil Nutrient Cycling ◽  
Growth Properties

Background Exploring high-quality organic amendments has been a focus of sustainable agriculture. Filtered mud (FM), a sugar factory waste derived from sugarcane stems, could be an alternative organic amendment for sugarcane production. However, the effects of its application proportions on soil fertility, nutrient cycling, structure of soil bacterial and fungal communities, and the growth of sugarcane in clay-loam soils remain unexplored. Methods Three application proportions of FM: (FM1-(FM: Soil at 1:4), FM2-(FM: Soil at 2:3), and FM3-(FM: Soil at 3:2)) were evaluated on sugarcane growth and soil nutrient cycling. High throughput sequencing was also employed to explore soil microbial dynamics. Results We observed that FM generally increased the soil’s nutritional properties while improving NO3− retention compared to the control, resulting in increased growth parameters of sugarcane. Specifically, FM1 increased the concentration of NH4+−N, the N fraction preferably taken up by sugarcane, which was associated with an increase in the plant height, and more improved growth properties, among other treatments. An increase in the proportion of FM also increased the activity of soil nutrient cycling enzymes; urease, phosphatase, and β-glucosidase. High throughput sequencing revealed that FM reduced the diversity of soil bacteria while having insignificant effects on fungal diversity. Although increasing FM rates reduced the relative abundance of the phyla Proteobacteria, its class members, the Gammaproteobacteria and Betaproteobacteria containing some N-cycling related genera, were stimulated. Also, FM stimulated the abundance of beneficial and lignocellulose degrading organisms. These included the bacterial phyla Actinobacteria, Bacteroidetes, Acidobacteria, Chloroflexi, and the fungal phylum Ascomycota. The distribution of the soil microbial community under FM rates was regulated by the changes in soil pH and the availability of soil nutrients. Since FM1 showed more promise in improving the growth properties of sugarcane, it could be more economical and sustainable for sugarcane production in clay-loam soils.

scholarly journals TAXONOMIC STRUCTURE OF PROKARYOTIC COMMUNITIES IN SOILS OF DIFFERENT BIOCLIMATIC ZONES

2018 ◽  
pp. 125-153 ◽  
Author(s):  
I. A. Tikhonovich ◽  
T. I. Chernov ◽  
A. D. Zhelezova ◽  
A. K. Tkhakakhova ◽  
E. E. Andronov ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Profile Analysis ◽  
Chestnut Soil ◽  
Diversity Indices ◽  
Taxonomic Structure ◽  
Typical Chernozem ◽  
Bacterial Phyla ◽  
Dry Steppe ◽  
Full Profile ◽  
The Difference

Using high-throughput sequencing, we performed a full-profile analysis of the taxonomic structure and diversity of prokaryotic communities of zonal soil series: sod-podzolic, dark gray, typical chernozem, brown soil, meadow-chestnut soil and solonets. Phyla Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, Planctomycetes, Proteobacteria and Verrucomicrobia formed up to 95% of prokaryotic communities in all studied soil horizons. Phyla Proteobacteria and Actinobacteria and archaeal phylum Thaumarchaeota dominated in all soils. We revealed the trends of changes in the representation of bacterial phyla in the soils of the zonal range from taiga to dry-steppe: a decrease of Acidobacteria and an increase of Actinobacteria in the upper horizons. The diversity indices of the prokaryotic communities of different genetic horizons of the studied soils were evaluated. In all soils, a decrease in diversity indices with the depth of the horizon was revealed. In all soils, a decrease in diversity indices with depth of the horizon was found, with a rare and slight increase in some lower horizons: structural metamorphic (BM), textural (BT) or accumulative carbonate (BCA) horizons. When examining the prokaryotic communities of soils with different genesis, no determining influence of pH and organic matter contents on the diversity indices was found. Differences in the taxonomic structure and diversity of prokaryotic communities of soils of different bioclimatic zones were presented due to a combination of factors: the difference in chemical and physical properties of soils, as well as in water and temperature conditions.

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