scholarly journals First Insights into the Microbiome of a Mangrove Tree Reveal Significant Differences in Taxonomic and Functional Composition among Plant and Soil Compartments

2019 ◽  
Vol 7 (12) ◽  
pp. 585 ◽  
Author(s):  
Witoon Purahong ◽  
Dolaya Sadubsarn ◽  
Benjawan Tanunchai ◽  
Sara Fareed Mohamed Wahdan ◽  
Chakriya Sansupa ◽  
...  
Keyword(s):  
Community Composition ◽  
Rhizosphere Soil ◽  
Plant Root ◽  
Nifh Gene ◽  
Nitrogen Fixing ◽  
Ecological Functions ◽  
Rhizophora Stylosa ◽  
Bacterial Phyla ◽  
Mangrove Tree ◽  
Mangrove Ecosystems

Mangrove forest trees play important ecological functions at the interface between terrestrial and marine ecosystems. However, despite playing crucial roles in plant health and productivity, there is little information on microbiomes of the tree species in mangrove ecosystems. Thus, in this study we aimed to characterize the microbiome in soil (rhizosphere) and plant (root, stem, and leaf endosphere) compartments of the widely distributed mangrove tree Rhizophora stylosa. Surprisingly, bacterial operational taxonomic units (OTUs) were only confidently detected in rhizosphere soil, while fungal OTUs were detected in all soil and plant compartments. The major detected bacterial phyla were affiliated to Proteobacteria, Actinobacteria, Planctomycetes, and Chloroflexi. Several nitrogen-fixing bacterial OTUs were detected, and the presence of nitrogen-fixing bacteria was confirmed by nifH gene based-PCR in all rhizosphere soil samples, indicating their involvement in N acquisition in the focal mangrove ecosystem. We detected taxonomically (54 families, 83 genera) and functionally diverse fungi in the R. stylosa mycobiome. Ascomycota (mainly Dothideomycetes, Eurotiomycetes, Sordariomycetes) were most diverse in the mycobiome, accounting for 86% of total detected fungal OTUs. We found significant differences in fungal taxonomic and functional community composition among the soil and plant compartments. We also detected significant differences in fungal OTU richness (p < 0.002) and community composition (p < 0.001) among plant compartments. The results provide the first information on the microbiome of rhizosphere soil to leaf compartments of mangrove trees and associated indications of ecological functions in mangrove ecosystems.

Phylogenetic diversity of nitrogen-fixing bacteria and thenifHgene from mangrove rhizosphere soil

2012 ◽  
Vol 58 (4) ◽  
pp. 531-539 ◽  
Author(s):  
Jianyin Liu ◽  
Mengjun Peng ◽  
Youguo Li
Keyword(s):  
Phylogenetic Trees ◽  
Rhizosphere Soil ◽  
Nifh Gene ◽  
Soil Samples ◽  
Community Diversity ◽  
Nitrogen Fixing ◽  
Pcr Cloning ◽  
Nitrogen Fixing Bacteria ◽  
Soil Dna ◽  
Mangrove Ecosystems

Nine types of nitrogen-fixing bacterial strains were isolated from 3 rhizosphere soil samples taken from mangrove plants in the Dongzhaigang National Mangrove Nature Reserve of China. Most isolates belonged to Gammaproteobacteria Pseudomonas , showing that these environments constituted favorable niches for such abundant nitrogen-fixing bacteria. New members of the diazotrophs were also found. Using a soil DNA extraction and PCR-cloning-sequencing approach, 135 clones were analyzed by restriction fragment length polymorphism (RFLP) analysis, and 27 unique nifH sequence phylotypes were identified, most of which were closely related to sequences from uncultured bacteria. The diversity of nitrogen-fixing bacteria was assessed by constructing nifH phylogenetic trees from sequences of all isolates and clones in this work, together with related nifH sequences from other mangrove ecosystems in GenBank. The nifH diversity varied among soil samples, with distinct biogeochemical properties within a mangrove ecosystem. When comparing different mangrove ecosystems, the nifH gene sequences from a specific site tended to cluster as individual groups. The results provided interesting data and novel information on our understanding of diazotroph community diversity in the mangrove ecosystems.

scholarly journals High-methionine soybean has no significant effect on nitrogen-transforming bacteria in rhizosphere soil

2018 ◽  
Vol 64 (No. 3) ◽  
pp. 108-113 ◽  
Author(s):  
Liang Jingang ◽  
Luan Ying ◽  
Jiao Yue ◽  
Sun Shi ◽  
Wu Cunxiang ◽  
...  
Keyword(s):  
Community Composition ◽  
Rhizosphere Soil ◽  
Microbial Community Composition ◽  
Potential Effect ◽  
Ammonia Oxidizing Bacteria ◽  
Nitrogen Fixing ◽  
Transgenic Soybean ◽  
Bacterial Populations ◽  
Microbial Functional Groups ◽  
Microbial Groups

Transgenic plants may induce shifts in the microbial community composition that in turn alter microbially-mediated nutrient cycling in soil. Studies of how specific microbial groups respond to genetically modified (GM) planting help predict potential impacts upon processes performed by these groups. This study investigated the effect of transgenic high-methionine soybean cv. ZD91 on nitrogen-fixing and ammonia-oxidizing bacterial populations. A difference in nitrogen-fixing or ammonia-oxidizing bacteria community composition was not found, suggesting that cv. ZD91 does not alter the bacterial populations in rhizosphere soil. This study increases our understanding of the potential effect of transgenic soybean on microbial functional groups within soil by suggesting that nitrogen-transforming bacteria may be useful for future investigations on the GM crops impact in the soil ecosystem.

scholarly journals Diversity pattern of nitrogen fixing microbes in nodules of <i>Trifolium arvense</i> (L.) at different initial stages of ecosystem development

2012 ◽  
Vol 9 (9) ◽  
pp. 13135-13160
Author(s):  
S. Schulz ◽  
M. Engel ◽  
D. Fischer ◽  
F. Buegger ◽  
M. Elmer ◽  
...  
Keyword(s):  
Community Composition ◽  
Nifh Gene ◽  
Ecosystem Development ◽  
Nitrogen Fixing ◽  
Clone Libraries ◽  
Carbon And Nitrogen ◽  
Soil Age ◽  
Trifolium Arvense ◽  
Nitrogen Contents ◽  
The Impact

Abstract. Legumes can be considered as pioneer plants during ecosystem development, as they form a symbiosis with different nitrogen fixing rhizobia species, which enable the plants to grow on soils with low available nitrogen content. In this study we compared the abundance and diversity of nitrogen fixing microbes based on the functional marker gene nifH, which codes for a subunit of the Fe-protein of the dinitrogenase reductase, in nodules of different size classes of Trifolium arvense (L.). Additionally, carbon and nitrogen contents of the bulk soil and plant material were measured. Plants were harvested from different sites, reflecting 2 (2a) and 5 (5a) yr of ecosystem development, of an opencast lignite mining area in the south of Cottbus, Lower Lusatia (Germany) where the artificial catchment "Chicken Creek" was constructed to study the development of terrestrial ecosystems. Plants from the 5a site revealed higher amounts of carbon and nitrogen, although nifH gene abundances in the nodules and carbon and nitrogen contents between the two soils did not differ significantly. Analysis of the nifH clone libraries showed a significant effect of the nodule size on the community composition of nitrogen fixing microbes. Medium sized nodules (2–5 mm) contained a uniform community composed of Rhizobium leguminosarum bv. trifolii, whereas the small nodules (< 2 mm) consisted of a diverse community including clones with non-Rhizobium nifH gene sequences. Regarding the impact of the soil age on the community composition a clear distinction between the small and the medium nodules can be made. While clone libraries from the medium nodules were pretty similar at both soil ages, soil age had a significant effect on the community compositions of the small nodules, where the proportion of R. leguminosarum bv. trifolii increased with soil age.

scholarly journals Diversity pattern of nitrogen fixing microbes in nodules of <i>Trifolium arvense</i> (L.) at different initial stages of ecosystem development

2013 ◽  
Vol 10 (2) ◽  
pp. 1183-1192 ◽  
Author(s):  
S. Schulz ◽  
M. Engel ◽  
D. Fischer ◽  
F. Buegger ◽  
M. Elmer ◽  
...  
Keyword(s):  
Community Composition ◽  
Nifh Gene ◽  
Ecosystem Development ◽  
Nitrogen Fixing ◽  
Clone Libraries ◽  
Carbon And Nitrogen ◽  
Soil Age ◽  
Trifolium Arvense ◽  
Nitrogen Contents ◽  
The Impact

Abstract. Legumes can be considered as pioneer plants during ecosystem development, as they form a symbiosis with different nitrogen fixing rhizobia species, which enable the plants to grow on soils with low available nitrogen content. In this study we compared the abundance and diversity of nitrogen fixing microbes based on the functional marker gene nifH, which codes for a subunit of the Fe-protein of the dinitrogenase reductase, in nodules of different size classes of Trifolium arvense (L.). Additionally, carbon and nitrogen contents of the bulk soil and plant material were measured. Plants were harvested from different sites, reflecting 2 (2a) and 5 (5a) yr of ecosystem development, of an opencast lignite mining area in the south of Cottbus, Lower Lusatia (Germany) where the artificial catchment "Chicken Creek" was constructed to study the development of terrestrial ecosystems. Plants from the 5a site revealed higher amounts of carbon and nitrogen, although nifH gene abundances in the nodules and carbon and nitrogen contents between the two soils did not differ significantly. Analysis of the nifH clone libraries showed a significant effect of the nodule size on the community composition of nitrogen fixing microbes. Medium sized nodules (2–5 mm) contained a uniform community composed of Rhizobium leguminosarum bv. trifolii, whereas the small nodules (<2 mm) consisted of a diverse community including clones with non-Rhizobium nifH gene sequences. Regarding the impact of the soil age on the community composition a clear distinction between the small and the medium nodules can be made. While clone libraries from the medium nodules were pretty similar at both soil ages, soil age had a significant effect on the community compositions of the small nodules, where the proportion of R. leguminosarum bv. trifolii increased with soil age.

scholarly journals Community of Mangrove Category Tree and Sapling in The Sekotong Bay, West Lombok

2021 ◽  
Vol 21 (2) ◽  
pp. 441
Author(s):  
Lalu Japa ◽  
Karnan Karnan ◽  
Didik Santoso
Keyword(s):  
Species Composition ◽  
Community Composition ◽  
Average Density ◽  
Rhizophora Stylosa ◽  
Mangrove Tree ◽  
Rhizophora Apiculata ◽  
Ceriops Tagal ◽  
Percentage Covering

Community of mangrove in the Bay of Sekotong, West Lombok was studied to know the species composition, individual density of each species, and percentage covering of mangrove canopy. Total 28 plots of 10 m x 10 m were set in 9 transects in 5 stations. Photographs of canopy covering and mangrove community composition were analyzed by using software ImageJ and template spreadsheet 10x10, the new version of March 2018. The community of mangrove of Sekotong bay, West Lombok consists of 8 species, 5 genera, and 4 families. Rhizophora apiculata & Rhizophora stylosa were recorded in seven of nine transects (78% of transect).  Ceriops tagal was a species that was also recorded to have the highest density (3700 trees/ha) in transect SKTM02B. The average density of the mangrove sapling category was higher than the mangrove tree category. The three highest covering percentages of canopi mangrove community took place in transects SKTM01A, SKTM01B, and SKTM04T.

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.

Grazing intensity rather than host plant’s palatability shape the community of arbuscular mycorrhizal fungi in a steppe grassland

2021 ◽  
Author(s):  
Maede Faghihinia ◽  
Yi Zou ◽  
Yongfei Bai ◽  
Martin Dudáš ◽  
Rob Marrs ◽  
...  
Keyword(s):  
Arbuscular Mycorrhizal Fungi ◽  
Community Composition ◽  
Mycorrhizal Fungi ◽  
Rhizosphere Soil ◽  
Grazing Intensity ◽  
Arbuscular Mycorrhizal ◽  
Grass Species ◽  
Α Diversity ◽  
Steppe Grassland

Abstract Arbuscular mycorrhizal fungi (AMF) are the predominant type of mycorrhizal fungi in roots and rhizosphere soil of grass species worldwide. Grasslands are currently experiencing increasing grazing pressure, but it is not yet clear how grazing intensity and host plant grazing preference by large herbivores interact with soil- and root-associated AMF communities. Here, we tested whether the diversity and community composition of AMF in the roots and rhizosphere soil of two dominant perennial grasses grazed differently by livestock change in response to grazing intensity. We conducted a study in a long-term field experiment in which seven levels of field-manipulated grazing intensities were maintained for 13 years in a typical steppe grassland in northern China. We extracted DNA from the roots and rhizosphere soil of two dominant grasses, Leymus chinense (Trin.) Tzvel. and Stipa grandis P. Smirn, with contrasting grazing preference by sheep. AMF DNA from root and soil samples were then subjected to molecular analysis. Our results showed that AMF α-diversity (richness) at the virtual taxa (VT) level varied as a function of grazing intensity. Different VTs showed completely different responses along the gradient, one increasing, one decreasing and others showing no response. Glomeraceae was the most abundant AMF family along the grazing gradient, which fits well with the theory of disturbance tolerance of this group. In addition, sheep grazing preference for host plants did not explain a considerable variation in AMF α-diversity. However, the two grass species exhibited different community composition in their roots and rhizosphere soils. Roots exhibited a lower α-diversity and higher β-diversity within the AMF community than soils. Overall, our results suggest that long-term grazing intensity might have changed the abundance of functionally-diverse AMF taxa in favor of those with disturbance-tolerant traits. We suggest our results would be useful in informing the choice of mycorrhizal fungi indicator variables when assessing the impacts of grassland management choices on grassland ecosystem functioning.

scholarly journals High diversity of nitrogen-fixing bacteria in the upper reaches of the Heihe River, northwestern China

2013 ◽  
Vol 10 (8) ◽  
pp. 5589-5600 ◽  
Author(s):  
X. S. Tai ◽  
W. L. Mao ◽  
G. X. Liu ◽  
T. Chen ◽  
W. Zhang ◽  
...  
Keyword(s):  
Water Conservation ◽  
Bacterial Communities ◽  
Nifh Gene ◽  
Qilian Mountains ◽  
Northwestern China ◽  
Heihe River ◽  
Meadow Soil ◽  
Nitrogen Fixing ◽  
Nitrogen Fixing Bacteria ◽  
Gene Copies

Abstract. Vegetation plays a key role in water conservation in the southern Qilian Mountains (northwestern China), located in the upper reaches of the Heihe River. Nitrogen-fixing bacteria are crucial for the protection of the nitrogen supply for vegetation in the region. In the present study, nifH gene clone libraries were established to determine differences between the nitrogen-fixing bacterial communities of the Potentilla parvifolia shrubland and the Carex alrofusca meadow in the southern Qilian Mountains. All of the identified nitrogen-fixing bacterial clones belonged to the Proteobacteria. At the genus level, Azospirillum was only detected in the shrubland soil, while Thiocapsa, Derxia, Ectothiorhodospira, Mesorhizobium, Klebsiella, Ensifer, Methylocella and Pseudomonas were only detected in the meadow soil. The phylogenetic tree was divided into five lineages: lineages I, II and III mainly contained nifH sequences obtained from the meadow soils, while lineage IV was mainly composed of nifH sequences obtained from the shrubland soils. The Shannon–Wiener index of the nifH genes ranged from 1.5 to 2.8 and was higher in the meadow soils than in the shrubland soils. Based on these analyses of diversity and phylogeny, the plant species were hypothesised to influence N cycling by enhancing the fitness of certain nitrogen-fixing taxa. The number of nifH gene copies and colony-forming units (CFUs) of the cultured nitrogen-fixing bacteria were lower in the meadow soils than in the shrubland soils, ranging from 0.4 × 107 to 6.9 × 107 copies g−1 soil and 0.97 × 106 to 12.78 × 106 g−1 soil, respectively. Redundancy analysis (RDA) revealed that the diversity and number of the nifH gene copies were primarily correlated with aboveground biomass in the shrubland soil. In the meadow soil, nifH gene diversity was most affected by altitude, while copy number was most impacted by soil-available K. These results suggest that the nitrogen-fixing bacterial communities beneath Potentilla were different from those beneath Carex.

scholarly journals Continuous monocropping highly affect the composition and diversity of microbial communities in peanut (Arachis hypogaea L.)

2021 ◽  
Vol 49 (4) ◽  
pp. 12532
Author(s):  
Ali I. MALLANO ◽  
Xianli ZHAO ◽  
Yanling SUN ◽  
Guangpin JIANG ◽  
Huang CHAO
Keyword(s):  
Microbial Communities ◽  
Management Practices ◽  
Rhizosphere Soil ◽  
Diversity Index ◽  
Cropping Systems ◽  
Soil Microbial Communities ◽  
Pathogenic Fungi ◽  
Continuous Cropping ◽  
Bacterial Phyla ◽  
Soil Microbial

Continuous cropping systems are the leading cause of decreased soil biological environments in terms of unstable microbial population and diversity index. Nonetheless, their responses to consecutive peanut monocropping cycles have not been thoroughly investigated. In this study, the structure and abundance of microbial communities were characterized using pyrosequencing-based approach in peanut monocropping cycles for three consecutive years. The results showed that continuous peanut cultivation led to a substantial decrease in soil microbial abundance and diversity from initial cropping cycle (T1) to later cropping cycle (T3). Peanut rhizosphere soil had Actinobacteria, Protobacteria, and Gemmatimonadetes as the major bacterial phyla. Ascomycota, Basidiomycota were the major fungal phylum, while Crenarchaeota and Euryarchaeota were the most dominant phyla of archaea. Several bacterial, fungal and archaeal taxa were significantly changed in abundance under continuous peanut cultivation. Bacterial orders, Actinomycetales, Rhodospirillales and Sphingomonadales showed decreasing trends from T1>T2>T3. While, pathogenic fungi Phoma was increased and beneficial fungal taxa Glomeraceae decreased under continuous monocropping. Moreover, Archaeal order Nitrososphaerales observed less abundant in first two cycles (T1&T2), however, it increased in third cycle (T3), whereas, Thermoplasmata exhibit decreased trends throughout consecutive monocropping. Taken together, we have shown the taxonomic profiles of peanut rhizosphere communities that were affected by continuous peanut monocropping. The results obtained from this study pave ways towards a better understanding of the peanut rhizosphere soil microbial communities in response to continuous cropping cycles, which could be used as bioindicator to monitor soil quality, plant health and land management practices.

scholarly journals OPTIMALISASI PRODUKSI ENZIM KITINASE PADA ISOLAT JAMUR KITINOLITIK DARI SAMPEL TANAH RIZOSFER

2018 ◽  
Vol 3 (01) ◽  
pp. 62-69
Author(s):  
Eka Corneliyawati ◽  
Massora Massora ◽  
Khikmah Khikmah ◽  
As’ad Syamsul Arifin
Keyword(s):  
Biological Control ◽  
Cell Wall ◽  
Rhizosphere Soil ◽  
Plant Root ◽  
Optimal Growth ◽  
Chitinase Activity ◽  
Fungal Species ◽  
Plant Roots ◽  
Chitinase Production

The rhizosphere is the zone of soil surrounding a plant root where plant roots, soil and the soil biota interact with each other. Chitinolytic fungi has been effectively used in biological control agens. The chitinase activity causes lysis of the fungi cell wall pathogen. The aim of the research was to find optimization of activity chitinase enzyme from rhizosphere soil was conducted in vitro. Optimal growth chitinase production for TKR3 fungi isolate were concentration of chitin 0,2% (b/v), pH 5,5, temperature 30ºC, agitation 150 rpm and incubation time at four days. The optimum yield of chitinase production is influenced by fungal species and environmental conditions.

Sign in / Sign up

Export Citation Format

Share Document