scholarly journals The Aromatic Plant Clary Sage Shaped Bacterial Communities in the Roots and in the Trace Element-Contaminated Soil More Than Mycorrhizal Inoculation – A Two-Year Monitoring Field Trial

2020 ◽  
Vol 11 ◽  
Author(s):  
Robin Raveau ◽  
Joël Fontaine ◽  
Mohamed Hijri ◽  
Anissa Lounès-Hadj Sahraoui
Keyword(s):  
Community Structure ◽  
Bacterial Diversity ◽  
Contaminated Soil ◽  
Mycorrhizal Fungi ◽  
Agricultural Soils ◽  
Illumina Miseq ◽  
Added Value ◽  
Rrna Gene ◽  
Aromatic Plants ◽  
Mycorrhizal Inoculation

To cope with soil contamination by trace elements (TE), phytomanagement has attracted much attention as being an eco-friendly and cost-effective green approach. In this context, aromatic plants could represent a good option not only to immobilize TE, but also to use their biomass to extract essential oils, resulting in high added-value products suitable for non-food valorization. However, the influence of aromatic plants cultivation on the bacterial community structure and functioning in the rhizosphere microbiota remains unknown. Thus, the present study aims at determining in TE-aged contaminated soil (Pb – 394 ppm, Zn – 443 ppm, and Cd – 7ppm, respectively, 11, 6, and 17 times higher than the ordinary amounts in regional agricultural soils) the effects of perennial clary sage (Salvia sclarea L.) cultivation, during two successive years of growth and inoculated with arbuscular mycorrhizal fungi, on rhizosphere bacterial diversity and community structure. Illumina MiSeq amplicon sequencing targeting bacterial 16S rRNA gene was used to assess bacterial diversity and community structure changes. Bioinformatic analysis of sequencing datasets resulted in 4691 and 2728 bacterial Amplicon Sequence Variants (ASVs) in soil and root biotopes, respectively. Our findings have shown that the cultivation of clary sage displayed a significant year-to-year effect, on both bacterial richness and community structures. We found that the abundance of plant-growth promoting rhizobacteria significantly increased in roots during the second growing season. However, we didn’t observe any significant effect of mycorrhizal inoculation neither on bacterial diversity nor on community structure. Our study brings new evidence in TE-contaminated areas of the effect of a vegetation cover with clary sage cultivation on the microbial soil functioning.

scholarly journals Spatial and Temporal Variation in Microbial Diversity and Community Structure in a Contaminated Mangrove Wetland

2020 ◽  
Vol 10 (17) ◽  
pp. 5850
Author(s):  
Jiaojiao Ma ◽  
Ting Zhou ◽  
Chunyu Xu ◽  
Dawen Shen ◽  
Songjun Xu ◽  
...  
Keyword(s):  
Community Structure ◽  
Spatial Variation ◽  
Temporal Variation ◽  
Bacterial Diversity ◽  
Diversity Index ◽  
Total Carbon ◽  
Spatial And Temporal Variation ◽  
Rrna Gene ◽  
Mangrove Wetland ◽  
Mangrove Soils

Field and laboratory investigations were conducted to characterize bacterial diversity and community structure in a badly contaminated mangrove wetland adjacent to the metropolitan area of a megacity in subtropical China. Next-generation sequencing technique was used for sequencing the V4–V5 region of the 16s rRNA gene on the Illumina system. Collectively, Proteobacteria, Chloroflexi, Planctomycetes, Actinobacteria and Bacteroidetes were the predominant phyla identified in the investigated soils. A significant spatial variation in bacterial diversity and community structure was observed for the investigated mangrove soils. Heavy metal pollution played a key role in reducing the bacterial diversity. The spatial variation in soil-borne heavy metals shaped the spatial variation in bacterial diversity and community structure in the study area. Other environmental factors such as total carbon and total nitrogen in the soils that are affected by seasonal change in temperature could also influence the bacterial abundance, diversity and community structure though the temporal variation was relatively weaker, as compared to spatial variation. The bacterial diversity index was lower in the investigated site than in the comparable reference site with less contaminated status. The community structure in mangrove soils at the current study site was, to a remarkable extent, different from those in the tropical mangrove wetlands around the world.

Mycorrhizal inoculation and application of Fe correction in the soil for ameliorating grapevine performance in a copper-contaminated soil

2021 ◽  
Author(s):  
Amaia Nogales ◽  
Erika S. Santos ◽  
Gonçalo Victorino ◽  
Wanda Viegas ◽  
Maria Manuela Abreu
Keyword(s):  
Soil Contamination ◽  
Contaminated Soil ◽  
Contaminated Soils ◽  
Mycorrhizal Fungi ◽  
Root Biomass ◽  
Arbuscular Mycorrhizal ◽  
Nutrient Contents ◽  
Beneficial Effects ◽  
Continuous Application ◽  
Mycorrhizal Inoculation

<p>Copper-based fungicides are commonly applied in vineyards to control fungal diseases that can severely affect grapevine productivity. Continuous application of this type of fungicides contributes to Cu accumulation in surface horizons of the soil, which can generate toxicity problems in plants, regardless of being an essential nutrient. Several strategies have been proposed to immobilize or counteract the effect of soil contaminants, such as plant inoculation with arbuscular mycorrhizal fungi (AMF). However, depending on the element concentration, this may not be sufficient to avoid its excessive accumulation in belowground and/or aboveground organs. Since Fe is known to have an antagonistic interaction with Cu in plants, Fe application, as an amendment, in vineyard soils, could be a good strategy to avoid excessive Cu uptake by grapevines growing in Cu-contaminated soils. However, little information is available on the combined effects of both strategies.</p><p>In order to reveal the possible beneficial effects of plant mycorrhization and Fe application in Cu-contaminated soils on grapevine growth and nutrition, a mesocosm experiment was established under controlled conditions. Two-year-old plants, previously inoculated or not with two different AMF, were grown in pots filled with 6.5 kg of an Arenosol collected from a wine-growing region. These plants were subjected to three soil treatments: 1) soil contamination with Cu, where the grapevines were watered with a solution containing 5.89 mg/L CuSO<sub>4</sub> to ensure that the soil in each container reached 300 mg Cu/kg; 2) soil contamination with Cu + Fe addition, where the plants were watered with a solution that contained the same amount of CuSO<sub>4</sub> plus 0.38 mg/L of FeNaEDTA·3H<sub>2</sub>O to achieve 100 mg of Fe/kg soil; and 3) non-contaminated soil watered with deionized water. Four months later, at the end of the growing season, plant vegetative growth as well as leaf and root nutrient contents were analyzed.</p><p>Grapevines inoculated with AMF demonstrated a good level of tolerance to high Cu concentrations in soil, as they presented significantly higher root biomass than non-inoculated plants and Cu was mainly accumulated in the roots avoiding its translocation to the aerial part. However, when the Cu-contaminated soil was amended with Fe, a significant decrease was observed in root biomass in all mycorrhizal inoculation treatments and Cu was accumulated in grapevine leaves. Contrastingly, Fe application helped to avoid the excessive increase of Mn concentrations in leaf and roots that is commonly induced in Cu contaminated soils, which can be detrimental for grapevine growth.</p><p>These results demonstrated that mycorrhizal inoculation is a suitable strategy to promote grapevine growth in Cu-contaminated soils. However, special attention needs to be taken when applying amendments to correct Cu contamination, as the mycorrhizal status of plants may alter the expected outcome.</p><p> </p><div> <div> </div> </div>

Host identity is more important in structuring bacterial epiphytes than endophytes in a tropical mangrove forest

2020 ◽  
Vol 96 (4) ◽  
Author(s):  
Hui Yao ◽  
Xiang Sun ◽  
Chao He ◽  
Xing-Chun Li ◽  
Liang-Dong Guo
Keyword(s):  
Community Structure ◽  
Endophytic Bacteria ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Network Structures ◽  
Community Structures ◽  
Mangrove Species ◽  
Host Identity ◽  
Biodiversity Maintenance ◽  
Endophytic Bacterial Community

ABSTRACT Interactions between plants and microbes are involved in biodiversity maintenance, community stability and ecosystem functioning. However, differences in the community and network structures between phyllosphere epiphytic and endophytic bacteria have rarely been investigated. Here, we examined phyllosphere epiphytic and endophytic bacterial communities of six mangrove species using Illumina MiSeq sequencing of the 16S rRNA gene. The results revealed that the community structure of epiphytic and endophytic bacteria was different. Plant identity significantly affected the diversity and community structure of both epiphytic and endophytic bacteria, with a greater effect on the community structure of the former than the latter. Network analysis showed that both plant–epiphytic and plant–endophytic bacterial network structures were characterized by significantly highly specialized and modular but lowly connected and anti-nested properties. Furthermore, the epiphytic bacterial network was more highly specialized and modular but less connected and more strongly anti-nested than the endophytic bacterial network. This study reveals that the phyllosphere epiphytic and endophytic bacterial community structures differ and plant identity has a greater effect on the epiphytic than on the endophytic bacteria, which may provide a comprehensive insight into the role of plant identity in driving the phyllosphere epiphytic and endophytic microbial community structures in mangrove ecosystems.

scholarly journals Phytate and Microbial Suspension Amendments Increased Soybean Growth and Shifted Microbial Community Structure

2021 ◽  
Vol 9 (9) ◽  
pp. 1803
Author(s):  
Bulbul Ahmed ◽  
Jean-Baptiste Floc’h ◽  
Zakaria Lahrach ◽  
Mohamed Hijri
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Indicator Species ◽  
Mycorrhizal Fungi ◽  
Rrna Gene ◽  
Soybean Plant ◽  
Trichoderma Spp ◽  
Undisturbed Soil ◽  
Microbial Suspension

Phytate represents an organic pool of phosphorus in soil that requires hydrolysis by phytase enzymes produced by microorganisms prior to its bioavailability by plants. We tested the ability of a microbial suspension made from an old growth maple forest’s undisturbed soil to mineralize phytate in a greenhouse trial on soybean plants inoculated or non-inoculated with the suspension. MiSeq Amplicon sequencing targeting bacterial 16S rRNA gene and fungal ITS was performed to assess microbial community changes following treatments. Our results showed that soybean nodulation and shoot dry weight biomass increased when phytate was applied to the nutrient-poor substrate mixture. Bacterial and fungal diversities of the root and rhizosphere biotopes were relatively resilient following inoculation by microbial suspension; however, bacterial community structure was significantly influenced. Interestingly, four arbuscular mycorrhizal fungi (AMF) were identified as indicator species, including Glomus sp., Claroideoglomus etunicatum, Funneliformis mosseae and an unidentified AMF taxon. We also observed that an ericoid mycorrhizal taxon Sebacina sp. and three Trichoderma spp. were among indicator species. Non-pathogenic Planctobacteria members highly dominated the bacterial community as core and hub taxa for over 80% of all bacterial datasets in root and rhizosphere biotopes. Overall, our study documented that inoculation with a microbial suspension and phytate amendment improved soybean plant growth.

scholarly journals Distribution of Hydrogen-Producing Bacteria in Tibetan Hot Springs, China

2021 ◽  
Vol 12 ◽  
Author(s):  
Li Ma ◽  
Geng Wu ◽  
Jian Yang ◽  
Liuqin Huang ◽  
Dorji Phurbu ◽  
...  
Keyword(s):  
Community Structure ◽  
Hydrogen Production ◽  
16S Rrna ◽  
High Throughput Sequencing ◽  
Hot Springs ◽  
Illumina Miseq ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
The Tibetan Plateau

Investigating the distribution of hydrogen-producing bacteria (HPB) is of great significance to understanding the source of biological hydrogen production in geothermal environments. Here, we explored the compositions of HPB populations in the sediments of hot springs from the Daggyai, Quzhuomu, Quseyongba, and Moluojiang geothermal zones on the Tibetan Plateau, with the use of Illumina MiSeq high-throughput sequencing of 16S rRNA genes and hydA genes. In the present study, the hydA genes were successfully amplified from the hot springs with a temperature of 46–87°C. The hydA gene phylogenetic analysis showed that the top three phyla of the HPB populations were Bacteroidetes (14.48%), Spirochaetes (14.12%), and Thermotogae (10.45%), while Proteobacteria were absent in the top 10 of the HPB populations, although Proteobacteria were dominant in the 16S rRNA gene sequences. Canonical correspondence analysis results indicate that the HPB community structure in the studied Tibetan hot springs was correlated with various environmental factors, such as temperature, pH, and elevation. The HPB community structure also showed a spatial distribution pattern; samples from the same area showed similar community structures. Furthermore, one HPB isolate affiliated with Firmicutes was obtained and demonstrated the capacity of hydrogen production. These results are important for us to understand the distribution and function of HPB in hot springs.

scholarly journals Bacterial diversity and community structure in nitrate-contaminated shallow groundwater in the Poyang Lake basin, China

2019 ◽  
Vol 98 ◽  
pp. 01012 ◽  
Author(s):  
Yihui Dong ◽  
Jiale Li ◽  
Zhanxue Sun ◽  
Evgeniya Soldatova ◽  
Jinjing Zan
Keyword(s):  
Community Structure ◽  
Bacterial Diversity ◽  
Poyang Lake ◽  
Shallow Groundwater ◽  
Jiangxi Province ◽  
Lake Basin ◽  
Rrna Gene ◽  
Bacterial Populations ◽  
Poyang Lake Basin ◽  
Groundwater Environment

The Poyang Lake basin in the Jiangxi province of China has been exposed to nitrate pollution caused by irrigation practices, leading to high groundwater nitrate concentration. Eight groundwater samples were collected from shallow wells for hydrochemical, bacterial diversity, and community structure analysis in November 2017. Shallow groundwaters of the basin are weakly acid and in an oxidizing state, with EC ranging from 87.6 to 279.5 µS/cm and TDS varying between 53 to 344 mg/L and averaging of 164 mg/L. The NO3-N form is the dominant nitrogen species in groundwater, with сoncentrations of NO3-N, NO2-N and NH4-N ranging between 2.5 to 164 mg/L, 0.01 to 0.10 mg/L, <0.01 to 0.08 mg/L, respectively. Groundwater communities are dominated by actinobacteria, alphaproteobacterial, gammaproteobacteria and betaproteobacteria both in high- and low-nitrate groundwaters. The results of a 16S rRNA gene clone library indicate that the bacterial community structure of the high-nitrate groundwater is different from that of the low-nitrate groundwater. The bacterial populations Denitratisoma and Sulfuritalea detected in low-nitrate groundwater suggest that these bacteria are capable of denitrification in anaerobic groundwater environment. Bacterial populations Flavobacteria and Cytophagia in high-nitrate groundwater are common in the s wetlands examined and likely capable of nitrification.

scholarly journals Identification of Microbial Profiles in Heavy-Metal-Contaminated Soil from Full-Length 16S rRNA Reads Sequenced by a PacBio System

2019 ◽  
Vol 7 (9) ◽  
pp. 357 ◽  
Author(s):  
Moonsuk Hur ◽  
Soo-Je Park
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Community Structure ◽  
16S Rrna ◽  
Microbial Communities ◽  
Contaminated Soil ◽  
Contaminated Soils ◽  
Full Length ◽  
Rrna Gene ◽  
Microbial Composition

Heavy metal pollution is a serious environmental problem as it adversely affects crop production and human activity. In addition, the microbial community structure and composition are altered in heavy-metal-contaminated soils. In this study, using full-length 16S rRNA gene sequences obtained by a PacBio RS II system, we determined the microbial diversity and community structure in heavy-metal-contaminated soil. Furthermore, we investigated the microbial distribution, inferred their putative functional traits, and analyzed the environmental effects on the microbial compositions. The soil samples selected in this study were heavily and continuously contaminated with various heavy metals due to closed mines. We found that certain microorganisms (e.g., sulfur or iron oxidizers) play an important role in the biogeochemical cycle. Using phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis, we predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) functional categories from abundances of microbial communities and revealed a high proportion belonging to transport, energy metabolism, and xenobiotic degradation in the studied sites. In addition, through full-length analysis, Conexibacter-like sequences, commonly identified by environmental metagenomics among the rare biosphere, were detected. In addition to microbial composition, we confirmed that environmental factors, including heavy metals, affect the microbial communities. Unexpectedly, among these environmental parameters, electrical conductivity (EC) might have more importance than other factors in a community description analysis.

scholarly journals Design and Evaluation of Illumina MiSeq-Compatible, 18S rRNA Gene-Specific Primers for Improved Characterization of Mixed Phototrophic Communities

2016 ◽  
Vol 82 (19) ◽  
pp. 5878-5891 ◽  
Author(s):  
Ian M. Bradley ◽  
Ameet J. Pinto ◽  
Jeremy S. Guest
Keyword(s):  
Community Structure ◽  
18S Rrna ◽  
Target Genes ◽  
Hypervariable Region ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Sequencing Bias ◽  
Primer Sets

ABSTRACTThe use of high-throughput sequencing technologies with the 16S rRNA gene for characterization of bacterial and archaeal communities has become routine. However, the adoption of sequencing methods for eukaryotes has been slow, despite their significance to natural and engineered systems. There are large variations among the target genes used for amplicon sequencing, and for the 18S rRNA gene, there is no consensus on which hypervariable region provides the most suitable representation of diversity. Additionally, it is unclear how much PCR/sequencing bias affects the depiction of community structure using current primers. The present study amplified the V4 and V8-V9 regions from seven microalgal mock communities as well as eukaryotic communities from freshwater, coastal, and wastewater samples to examine the effect of PCR/sequencing bias on community structure and membership. We found that degeneracies on the 3′ end of the current V4-specific primers impact read length and mean relative abundance. Furthermore, the PCR/sequencing error is markedly higher for GC-rich members than for communities with balanced GC content. Importantly, the V4 region failed to reliably capture 2 of the 12 mock community members, and the V8-V9 hypervariable region more accurately represents mean relative abundance and alpha and beta diversity. Overall, the V4 and V8-V9 regions show similar community representations over freshwater, coastal, and wastewater environments, but specific samples show markedly different communities. These results indicate that multiple primer sets may be advantageous for gaining a more complete understanding of community structure and highlight the importance of including mock communities composed of species of interest.IMPORTANCEThe quantification of error associated with community representation by amplicon sequencing is a critical challenge that is often ignored. When target genes are amplified using currently available primers, differential amplification efficiencies result in inaccurate estimates of community structure. The extent to which amplification bias affects community representation and the accuracy with which different gene targets represent community structure are not known. As a result, there is no consensus on which region provides the most suitable representation of diversity for eukaryotes. This study determined the accuracy with which commonly used 18S rRNA gene primer sets represent community structure and identified particular biases related to PCR amplification and Illumina MiSeq sequencing in order to more accurately study eukaryotic microbial communities.

scholarly journals Comparative Analysis of Gut Microbiota in Captive and Wild Oriental White Storks: Implications for Conservation Biology

2021 ◽  
Vol 12 ◽  
Author(s):  
Hong Wu ◽  
Fang-Ting Wu ◽  
Qi-Hai Zhou ◽  
Da-Peng Zhao
Keyword(s):  
Community Structure ◽  
Comparative Analysis ◽  
Gut Microbiota ◽  
Species Composition ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Α Diversity ◽  
White Storks

The oriental white stork (Ciconia boyciana) is considered an endangered species based on the International Union for Conservation of Nature (IUCN) Red List. This study presents the first evidence on comparative analysis of gut microbial diversity of C. boyciana from various breeding conditions. To determine the species composition and community structure of the gut microbiota, 24 fecal samples from Tianjin Zoo and Tianjin Qilihai Wetland were characterized by sequencing 16S rRNA gene amplicons using the Illumina MiSeq platform. Firmicutes was found to be the predominant phylum. Analysis of community structure revealed significant differences in the species diversity and richness between the populations of the two breeding conditions. The greatest α-diversity was found in wild C. boyciana, while artificial breeding storks from Tianjin Zoo had the least α-diversity. Principal coordinates analysis showed that the microbial communities were different between the two studied groups. In conclusion, this study reveals the species composition and structure of the gut microbiota of oriental white storks under two breeding conditions, and our findings could contribute to the integrative conservation of this endangered bird.

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