Diversity pattern of nitrogen fixing microbes in nodules of &lt;i&gt;Trifolium arvense&lt;/i&gt; (L.) at different initial stages of ecosystem development

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.

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

Biogeosciences Discussions ◽

10.5194/bgd-9-13135-2012 ◽

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.

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

Microorganisms ◽

10.3390/microorganisms7120585 ◽

2019 ◽

Vol 7 (12) ◽

pp. 585 ◽

Cited By ~ 1

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.

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Influence of environmental conditions and some soil chemical properties on the carbon and nitrogen contents of some tropical Australian rainforest soils

Soil Research ◽

10.1071/sr9900825 ◽

1990 ◽

Vol 28 (6) ◽

pp. 825 ◽

Cited By ~ 72

Author(s):

AV Spain

Keyword(s):

Chemical Properties ◽

Clay Content ◽

Free Iron ◽

Parent Materials ◽

Carbon And Nitrogen ◽

Temperature And Precipitation ◽

North Eastern ◽

Nitrogen Concentrations ◽

Soil Age ◽

Nitrogen Contents

Concentrations of carbon, total nitrogen, total phosphorus, soil pH, the sum of the exchangeable basic cations, clay and dithionite-extractable iron were examined in the surface soils of 72 rainforest sites from north-eastern tropical Queensland. Soils derived from basalt had higher levels of most of the above properties than those formed on other parent materials. Differences between the carbon status of soils formed from basalt and those formed from other parent materials may be related to the higher free iron levels and phosphorus status of the former group. Excluding the soils of basalt origin, both carbon and nitrogen are positively related to clay content. In contrast, within the soils of basaltic origin, carbon concentrations are negatively related to clay contents through interactions with free iron oxides. Separate univariate regression relationships were established between carbon and nitrogen concentrations and site temperature and precipitation for soils derived from basaltic and combined granitic and acid volcanic parent materials. Coefficients relating both nitrogen and carbon to temperature differed between these groupings. The importance of topography in controlling carbon levels is demonstrated in soils that are poorly drained or formed on ridges, while the importance of soil age is demonstrated by a juvenile soil formed on weakly weathered basalt.

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SULPHUR, CARBON, AND NITROGEN CONTENTS OF ORGANIC FRACTIONS FROM ACETYLACETONE EXTRACTS OF SOILS

Journal of Soil Science ◽

10.1111/j.1365-2389.1976.tb02003.x ◽

1976 ◽

Vol 27 (3) ◽

pp. 324-330 ◽

Cited By ~ 12

Author(s):

N. M. SCOTT ◽

G. ANDERSON

Keyword(s):

Carbon And Nitrogen ◽

Organic Fractions ◽

Nitrogen Contents

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Are Bacterio- and Phytoplankton Community Compositions Related in Lakes Differing in Their Cyanobacteria Contribution and Physico-Chemical Properties?

Genes ◽

10.3390/genes12060855 ◽

2021 ◽

Vol 12 (6) ◽

pp. 855

Author(s):

Mikołaj Kokociński ◽

Dariusz Dziga ◽

Adam Antosiak ◽

Janne Soininen

Keyword(s):

Environmental Factors ◽

Community Composition ◽

Phytoplankton Community ◽

Heterotrophic Bacteria ◽

Bacterial Community Composition ◽

Physical Factors ◽

Research Attention ◽

Phytoplankton Community Composition ◽

The Impact ◽

Bacteria Communities

Bacterioplankton community composition has become the center of research attention in recent years. Bacteria associated with toxic cyanobacteria blooms have attracted considerable interest. However, little is known about the environmental factors driving the bacteria community, including the impact of invasive cyanobacteria. Therefore, our aim has been to determine the relationships between heterotrophic bacteria and phytoplankton community composition across 24 Polish lakes with different contributions of cyanobacteria including the invasive species Raphidiopsis raciborskii. This analysis revealed that cyanobacteria were present in 16 lakes, while R. raciborskii occurred in 14 lakes. Our results show that bacteria communities differed between lakes dominated by cyanobacteria and lakes with minor contributions of cyanobacteria but did not differ between lakes with R. raciborskii and other lakes. Physical factors, including water and Secchi depth, were the major drivers of bacteria and phytoplankton community composition. However, in lakes dominated by cyanobacteria, bacterial community composition was also influenced by biotic factors such as the amount of R. raciborskii, chlorophyll-a and total phytoplankton biomass. Thus, our study provides novel evidence on the influence of environmental factors and R. raciborskii on lake bacteria communities.

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Genome-Wide Association Analysis Dissects the Genetic Basis of the Grain Carbon and Nitrogen Contents in Milled Rice

Rice ◽

10.1186/s12284-019-0362-2 ◽

2019 ◽

Vol 12 (1) ◽

Author(s):

Liang Tang ◽

Fan Zhang ◽

Anjin Liu ◽

Jian Sun ◽

Song Mei ◽

...

Keyword(s):

Association Analysis ◽

Genetic Basis ◽

Genome Wide Association ◽

Milled Rice ◽

Genome Wide Association Analysis ◽

Carbon And Nitrogen ◽

Genome Wide ◽

Nitrogen Contents

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Assessing Genotypic and Environmental Effects on Endophyte Communities of Fraxinus (Ash) Using Culture Dependent and Independent DNA Sequencing

Journal of Fungi ◽

10.3390/jof7070565 ◽

2021 ◽

Vol 7 (7) ◽

pp. 565

Author(s):

Anindita Lahiri ◽

Brian R. Murphy ◽

Trevor R. Hodkinson

Keyword(s):

Community Composition ◽

Environmental Effects ◽

High Throughput Sequencing ◽

Fungal Community Composition ◽

Species Identity ◽

Ash Dieback ◽

Hymenoscyphus Fraxineus ◽

Culture Independent ◽

The Impact ◽

Culture Dependent

Fraxinus excelsior populations are in decline due to the ash dieback disease Hymenoscyphus fraxineus. It is important to understand genotypic and environmental effects on its fungal microbiome to develop disease management strategies. To do this, we used culture dependent and culture independent approaches to characterize endophyte material from contrasting ash provenances, environments, and tissues (leaves, roots, seeds). Endophytes were isolated and identified using nrITS, LSU, or tef DNA loci in the culture dependent assessments, which were mostly Ascomycota and assigned to 37 families. Few taxa were shared between roots and leaves. The culture independent approach used high throughput sequencing (HTS) of nrITS amplicons directly from plant DNA and detected 35 families. Large differences were found in OTU diversity and community composition estimated by the contrasting approaches and these data need to be combined for estimations of the core endophyte communities. Species richness and Shannon index values were highest for the leaf material and the French population. Few species were shared between seed and leaf tissue. PCoA and NMDS of the HTS data showed that seed and leaf microbiome communities were highly distinct and that there was a strong influence of Fraxinus species identity on their fungal community composition. The results will facilitate a better understanding of ash fungal ecology and are a step toward identifying microbial biocontrol systems to minimize the impact of the disease.

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Postinoculation Protozoan Establishment and Association Patterns of Methanogenic Archaea in the Ovine Rumen

Applied and Environmental Microbiology ◽

10.1128/aem.02687-06 ◽

2007 ◽

Vol 73 (14) ◽

pp. 4609-4618 ◽

Cited By ~ 67

Author(s):

Samuel Ohene-Adjei ◽

Ronald M. Teather ◽

Michael Ivan ◽

Robert J. Forster

Keyword(s):

Phylogenetic Analysis ◽

Denaturing Gradient Gel Electrophoresis ◽

Methanogenic Archaea ◽

Type A ◽

Negative Control ◽

Rrna Gene ◽

Association Patterns ◽

Clone Libraries ◽

Symbiotic Relationships ◽

The Impact

ABSTRACT Association patterns between archaea and rumen protozoa were evaluated by analyzing archaeal 16S rRNA gene clone libraries from ovine rumen inoculated with different protozoa. Five protozoan inoculation treatments, fauna free (negative control), holotrich and cellulolytic protozoa, Isotricha and Dasytricha spp., Entodinium spp., and total fauna (type A) were tested. We used denaturing gradient gel electrophoresis, quantitative PCR, and phylogenetic analysis to evaluate the impact of the protozoan inoculants on the respective archaeal communities. Protozoan 18S ribosomal DNA clone libraries were also evaluated to monitor the protozoal population that was established by the inoculation. Phylogenetic analysis suggested that archaeal clones associated with the fauna-free, the Entodinium, and the type A inoculations clustered primarily with uncultured phylotypes. Polyplastron multivesiculatum was the predominant protozoan strain established by the holotrich and cellulolytic protozoan treatment, and this resulted predominantly in archaeal clones affiliated with uncultured and cultured methanogenic phylotypes (Methanosphaera stadtmanae, Methanobrevibacter ruminantium, and Methanobacterium bryantii). Furthermore, the Isotricha and Dasytricha inoculation treatment resulted primarily in archaeal clones affiliated with Methanobrevibacter smithii. This report provides the first assessment of the influence of protozoa on archaea within the rumen microbial community and provides evidence to suggest that different archaeal phylotypes associate with specific groups of protozoa. The observed patterns may be linked to the evolution of commensal and symbiotic relationships between archaea and protozoa in the ovine rumen environment. This report further underscores the prevalence and potential importance of a rather large group of uncultivated archaea in the ovine rumen, probably unrelated to known methanogens and undocumented in the bovine rumen.

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