scholarly journals Microbes follow Humboldt: temperature drives plant and soil microbial diversity patterns from the Amazon to the Andes

2016 ◽  
Author(s):  
Andrew T. Nottingham ◽  
Noah Fierer ◽  
Benjamin L. Turner ◽  
Jeanette Whitaker ◽  
Nick J. Ostle ◽  
...  
Keyword(s):  
Species Richness ◽  
Microbial Diversity ◽  
Tropical Forest ◽  
Soil Ph ◽  
Soil Bacteria ◽  
Environmental Drivers ◽  
Future Climate Change ◽  
Soil Microbial Diversity ◽  
Tropical Mountains ◽  
Bacteria And Fungi

SummaryMore than 200 years ago, von Humboldt reported decreases in tropical plant species richness with increasing elevation and decreasing temperature. Surprisingly, co-ordinated patterns in plant, bacterial and fungal diversity on tropical mountains are yet to be observed, despite the central role of soil microorganisms in terrestrial biogeochemistry. We studied an Andean transect traversing 3.5 km in elevation to test whether the species diversity and composition of tropical forest plants, soil bacteria and fungi can follow similar biogeographical patterns with shared environmental drivers. We found co-ordinated changes with elevation in all three groups: species richness declined as elevation increased, and the compositional-dissimilarity of communities increased with increased separation in elevation, although changes in plant diversity were larger than in bacteria and fungi. Temperature was the dominant driver of these diversity gradients, with weak influences of edaphic properties, including soil pH. The gradients in microbial diversity were strongly correlated with the activities of enzymes involved in organic matter cycling, and were accompanied by a transition in microbial traits towards slower-growing, oligotrophic taxa at higher elevations. We provide the first evidence of co-ordinated temperature-driven patterns in the diversity and distribution of three major biotic groups in tropical ecosystems: soil bacteria, fungi and plants. These findings suggest that, across landscape scales of relatively constant soil pH, inter-related patterns of plant and microbial communities with shared environmental drivers can occur, with large implications for tropical forest communities under future climate change.

scholarly journals History Leaves Its Mark on Soil Bacterial Diversity

mBio ◽  
2016 ◽  
Vol 7 (3) ◽  
Author(s):  
Jennifer B. H. Martiny
Keyword(s):  
Climate Change ◽  
Microbial Diversity ◽  
Bacterial Diversity ◽  
Soil Bacteria ◽  
Future Climate Change ◽  
Soil Bacterial Diversity ◽  
Soil Microbial Diversity ◽  
Climate Conditions ◽  
Soil Microbial ◽  
Evolutionary Diversification

ABSTRACT Dispersal is closely tied to the origin and maintenance of microbial diversity. With its focus on a narrow group of soil bacteria, recent work by Andam and colleagues on Streptomyces has provided perhaps the strongest support so far that some bacterial diversity in soils can be attributed to regional endemism (C. P. Andam et al., mBio 7:e02200-15, 2016, http://dx.doi.org/10.1128/mBio.02200-15 ). This means that dispersal is limited enough to allow for evolutionary diversification. Further analyses suggest that signatures of climate conditions more than 10,000 years ago can be detected in contemporary populations of this genus. These legacies have implications for how future climate change might alter soil microbial diversity.

scholarly journals Soil microbial diversity in organic and non-organic pasture systems

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11184
Author(s):  
Mohan Acharya ◽  
Amanda J. Ashworth ◽  
Yichao Yang ◽  
Joan M. Burke ◽  
Jung Ae Lee ◽  
...  
Keyword(s):  
Species Richness ◽  
Microbial Diversity ◽  
Bacterial Species ◽  
Soil Microbiome ◽  
Organic Soils ◽  
Pasture Management ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Organic Systems ◽  
Microbiome Diversity

Understanding the effects of organic pasture management on the soil microbiome is important for sustainable forage production since soil microbiome diversity contributes to improved nutrient cycling, soil structure, plant growth, and environmental resiliency; however, the soil microbiome response to pasture management is largely unknown. This study assessed the soil microbial diversity, richness, and community structure following 10 years of pasture management (organic or non-organic) of the V4 region of the 16S rRNA using the Illumina MiSeq platform. Soil samples were collected from 0–15 cm in July and August from 2017–2018 and soil nutrient properties (nutrients, carbon, nitrogen, and pH) quantified and correlated with soil microbial diversity. Overall, greater soil bacterial species richness (P ≤ 0.05) occurred in organic relative to non-organic (conventional) systems. Management affected bacterial species richness (Chao1), with greater richness occurring in organic pasture soils and less richness occurring in non-organic systems (P ≤ 0.05). Similarly, management affected bacterial evenness (Simpson’s index), with a more diverse community occurring in organically managed soils relative to non-organic pastures (P ≤ 0.05). Linear discriminant analysis effect size analysis showed statistically significant and biologically consistent differences in bacterial taxa in organic compared with non-organic soils. Therefore, there was a shift in bacterial community structure in organic relative to non-organic soils (P ≤ 0.05). Additionally, soil nutrients (Fe, Mg, Ni, S, Al, K, Cd, and Cu), pH, C, and N were correlated with one or more dominant bacterial phyla (Gemmatimonadetes, Planctomycetes, Firmicutes, Chloroflexi, Actinobacteria, and Acidobacteria). Overall, pasture management affected soil microbial diversity, with greater diversity occurring in organic than non-organic systems, likely owing to applications of organic poultry litter in organic systems compared to non-organic management (use of inorganic-fertilizers and herbicides). Results indicate that when pastures are converted to organic production systems, soil microbial richness and diversity may increase, thereby resulting in enhanced soil microbiome diversity and overall ecosystem services.

scholarly journals Plant Taxonomic Diversity Better Explains Soil Fungal and Bacterial Diversity than Functional Diversity in Restored Forest Ecosystems

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 479 ◽  
Author(s):  
Hanif ◽  
Guo ◽  
Moniruzzaman ◽  
He ◽  
Yu ◽  
...  
Keyword(s):  
Species Richness ◽  
Microbial Diversity ◽  
Soil Properties ◽  
Bacterial Diversity ◽  
Functional Diversity ◽  
Forest Ecosystems ◽  
Taxonomic Diversity ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Bacterial Richness

Plant attributes have direct and indirect effects on soil microbes via plant inputs and plant-mediated soil changes. However, whether plant taxonomic and functional diversities can explain the soil microbial diversity of restored forest ecosystems remains elusive. Here, we tested the linkage between plant attributes and soil microbial communities in four restored forests (Acacia species, Eucalyptus species, mixed coniferous species, mixed native species). The trait-based approaches were applied for plant properties and high-throughput Illumina sequencing was applied for fungal and bacterial diversity. The total number of soil microbial operational taxonomic units (OTUs) varied among the four forests. The highest richness of fungal OTUs was found in the Acacia forest. However, bacterial OTUs were highest in the Eucalyptus forest. Species richness was positively and significantly related to fungal and bacterial richness. Plant taxonomic diversity (species richness and species diversity) explained more of the soil microbial diversity than the functional diversity and soil properties. Prediction of fungal richness was better than that of bacterial richness. In addition, root traits explained more variation than the leaf traits. Overall, plant taxonomic diversity played a more important role than plant functional diversity and soil properties in shaping the soil microbial diversity of the four forests.

scholarly journals Linkage between tree species richness and soil microbial diversity improves phosphorus bioavailability

2019 ◽  
Vol 33 (8) ◽  
pp. 1549-1560 ◽  
Author(s):  
Huili Wu ◽  
Wenhua Xiang ◽  
Shuai Ouyang ◽  
David I. Forrester ◽  
Bo Zhou ◽  
...  
Keyword(s):  
Species Richness ◽  
Microbial Diversity ◽  
Tree Species ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Tree Species Richness

scholarly journals Changes in taxonomic and functional diversity of plants in a chronosequence of Eucalyptus grandis plantations

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Pamela E. Pairo ◽  
Estela E. Rodriguez ◽  
M. Isabel Bellocq ◽  
Pablo G. Aceñolaza
Keyword(s):  
Species Richness ◽  
Leaf Litter ◽  
Plant Species ◽  
Functional Diversity ◽  
Soil Ph ◽  
Management Practices ◽  
Environmental Changes ◽  
Canopy Cover ◽  
Environmental Drivers ◽  
Natural Grasslands

AbstractTree plantations have become one of the fastest-growing land uses and their impact on biodiversity was evaluated mainly at the taxonomic level. The aim of this study was to analyze environmental changes after the Eucalyptus plantation in an area originally covered by natural grasslands, taking into account the alpha and beta (taxonomic and functional) diversity of plant communities. We selected nine plantation ages, along a 12 years chronosequence, with three replicates per age and three protected grasslands as the original situation. At each replicate, we established three plots to measure plant species cover, diversity and environmental variables. Results showed that species richness, and all diversity indices, significantly declined with increasing plantation age. Canopy cover, soil pH, and leaf litter were the environmental drivers that drove the decrease in taxonomic and functional diversity of plants through the forest chronosequence. Based on the path analyses results, canopy cover had an indirect effect on plant functional diversity, mediated by leaf litter depth, soil pH, and plant species richness. The high dispersal potential, annual, barochorous, and zoochorous plant species were the functional traits more affected by the eucalypt plantations. We recommend two management practices: reducing forest densities to allow higher light input to the understory and, due to the fact that leaf litter was negatively associated with all diversity facets, we recommend reducing their accumulation or generate heterogeneity in its distribution to enhance biodiversity.

scholarly journals Increasing aridity reduces soil microbial diversity and abundance in global drylands

2015 ◽  
Vol 112 (51) ◽  
pp. 15684-15689 ◽  
Author(s):  
Fernando T. Maestre ◽  
Manuel Delgado-Baquerizo ◽  
Thomas C. Jeffries ◽  
David J. Eldridge ◽  
Victoria Ochoa ◽  
...  
Keyword(s):  
Climate Change ◽  
Soil Bacteria ◽  
Soil Microbial Communities ◽  
Terrestrial Ecosystems ◽  
Soil Microbial Diversity ◽  
Change Models ◽  
Soil Microbial ◽  
Soil Bacteria And Fungi ◽  
Abundance And Diversity ◽  
Bacteria And Fungi

Soil bacteria and fungi play key roles in the functioning of terrestrial ecosystems, yet our understanding of their responses to climate change lags significantly behind that of other organisms. This gap in our understanding is particularly true for drylands, which occupy ∼41% of Earth´s surface, because no global, systematic assessments of the joint diversity of soil bacteria and fungi have been conducted in these environments to date. Here we present results from a study conducted across 80 dryland sites from all continents, except Antarctica, to assess how changes in aridity affect the composition, abundance, and diversity of soil bacteria and fungi. The diversity and abundance of soil bacteria and fungi was reduced as aridity increased. These results were largely driven by the negative impacts of aridity on soil organic carbon content, which positively affected the abundance and diversity of both bacteria and fungi. Aridity promoted shifts in the composition of soil bacteria, with increases in the relative abundance of Chloroflexi and α-Proteobacteria and decreases in Acidobacteria and Verrucomicrobia. Contrary to what has been reported by previous continental and global-scale studies, soil pH was not a major driver of bacterial diversity, and fungal communities were dominated by Ascomycota. Our results fill a critical gap in our understanding of soil microbial communities in terrestrial ecosystems. They suggest that changes in aridity, such as those predicted by climate-change models, may reduce microbial abundance and diversity, a response that will likely impact the provision of key ecosystem services by global drylands.

scholarly journals Microbial Diversity Characteristics of Areca Palm Rhizosphere Soil at Different Growth Stages

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2706
Author(s):  
Siyuan Ma ◽  
Yubin Lin ◽  
Yongqiang Qin ◽  
Xiaoping Diao ◽  
Peng Li
Keyword(s):  
Microbial Diversity ◽  
Developmental Stages ◽  
Rhizosphere Soil ◽  
Interaction Network ◽  
Illumina Miseq ◽  
Growth Stages ◽  
Dominant Group ◽  
Soil Microbial Diversity ◽  
Bacteria And Fungi ◽  
Stage T1

The rhizosphere microflora are key determinants that contribute to plant health and productivity, which can support plant nutrition and resistance to biotic and abiotic stressors. However, limited research is conducted on the areca palm rhizosphere microbiota. To further study the effect of the areca palm’s developmental stages on the rhizosphere microbiota, the rhizosphere microbiota of areca palm (Areca catechu) grown in its main producing area were examined in Wanning, Hainan province, at different vegetation stages by an Illumina Miseq sequence analysis of the 16S ribosomal ribonucleic acid and internal transcribed spacer genes. Significant shifts of the taxonomic composition of the bacteria and fungi were observed in the four stages. Burkholderia-Caballeronia-Paraburkholderia were the most dominant group in stage T1 and T2; the genera Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium were decreased significantly from T1 to T2; and the genera Acidothermus and Bacillus were the most dominant in stage T3 and T4, respectively. Meanwhile, Neocosmospora, Saitozyma, Penicillium, and Trichoderma were the most dominant genera in the stage T1, T2, T3, and T4, respectively. Among the core microbiota, the dominant bacterial genera were Burkholderia-Caballeronia-Paraburkholderia and Bacillus, and the dominant fungal genera were Saitozyma and Trichoderma. In addition, we identified five bacterial genera and five fungal genera that reached significant levels during development. Finally, we constructed the OTU (top 30) interaction network of bacteria and fungi, revealed its interaction characteristics, and found that the bacterial OTUs exhibited more extensive interactions than the fungal OTUs. Understanding the rhizosphere soil microbial diversity characteristics of the areca palm could provide the basis for exploring microbial association and maintaining the areca palm’s health.

Community characteristics of forest understory birds along an elevational gradient in the Horn of Africa: A multi-year baseline

The Condor ◽  
2021 ◽  
Author(s):  
Kyle D Kittelberger ◽  
Montague H C Neate-Clegg ◽  
Evan R Buechley ◽  
Çağan Hakkı Şekercioğlu
Keyword(s):  
Species Richness ◽  
Species Turnover ◽  
Survival Rates ◽  
Elevational Gradient ◽  
Forest Understory ◽  
Bird Abundance ◽  
Tropical Mountains ◽  
Demographic Rates ◽  
Understory Birds ◽  
Over Time

Abstract Tropical mountains are global hotspots for birdlife. However, there is a dearth of baseline avifaunal data along elevational gradients, particularly in Africa, limiting our ability to observe and assess changes over time in tropical montane avian communities. In this study, we undertook a multi-year assessment of understory birds along a 1,750 m elevational gradient (1,430–3,186 m) in an Afrotropical moist evergreen montane forest within Ethiopia’s Bale Mountains. Analyzing 6 years of systematic bird-banding data from 5 sites, we describe the patterns of species richness, abundance, community composition, and demographic rates over space and time. We found bimodal patterns in observed and estimated species richness across the elevational gradient (peaking at 1,430 and 2,388 m), although no sites reached asymptotic species richness throughout the study. Species turnover was high across the gradient, though forested sites at mid-elevations resembled each other in species composition. We found significant variation across sites in bird abundance in some of the dietary and habitat guilds. However, we did not find any significant trends in species richness or guild abundances over time. For the majority of analyzed species, capture rates did not change over time and there were no changes in species’ mean elevations. Population growth rates, recruitment rates, and apparent survival rates averaged 1.02, 0.52, and 0.51 respectively, and there were no elevational patterns in demographic rates. This study establishes a multi-year baseline for Afrotropical birds along an elevational gradient in an under-studied international biodiversity hotspot. These data will be critical in assessing the long-term responses of tropical montane birdlife to climate change and habitat degradation.

scholarly journals A Degeneration Gradient of Poplar Trees Contributes to the Taxonomic, Functional, and Resistome Diversity of Bacterial Communities in Rhizosphere Soils

2021 ◽  
Vol 22 (7) ◽  
pp. 3438
Author(s):  
Juan Liu ◽  
Xiangwei He ◽  
Jingya Sun ◽  
Yuchao Ma
Keyword(s):  
Soil Fertility ◽  
Microbial Diversity ◽  
Resistance Genes ◽  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
Antibiotics Resistance ◽  
Plant Growth Promoting Bacteria ◽  
Soil Microbial Diversity ◽  
Antibiotic Target ◽  
And Function

Bacterial communities associated with roots influence the health and nutrition of the host plant. However, the microbiome discrepancy are not well understood under different healthy conditions. Here, we tested the hypothesis that rhizosphere soil microbial diversity and function varies along a degeneration gradient of poplar, with a focus on plant growth promoting bacteria (PGPB) and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG (antibiotics resistance genes) annotation revealed that available potassium (AK) was correlated with microbial diversity and function. We proposed several microbes, Bradyrhizobium, Sphingomonas, Mesorhizobium, Nocardioides, Variovorax, Gemmatimonadetes, Rhizobacter, Pedosphaera, Candidatus Solibacter, Acidobacterium, and Phenylobacterium, as candidates to reflect the soil fertility and the plant health. The highest abundance of multidrug resistance genes and the four mainly microbial resistance mechanisms (antibiotic efflux, antibiotic target protection, antibiotic target alteration, and antibiotic target replacement) in healthy poplar rhizosphere, corroborated the relationship between soil fertility and microbial activity. This result suggested that healthy rhizosphere soil harbored microbes with a higher capacity and had more complex microbial interaction network to promote plant growing and reduce intracellular levels of antibiotics. Our findings suggested a correlation between the plant degeneration gradient and bacterial communities, and provided insight into the role of high-turnover microbial communities as well as potential PGPB as real-time indicators of forestry soil quality, and demonstrated the inner interaction contributed by the bacterial communities.

scholarly journals Improvement of Soil Microbial Diversity through Sustainable Agricultural Practices and Its Evaluation by -Omics Approaches: A Perspective for the Environment, Food Quality and Human Safety

2021 ◽  
Vol 9 (7) ◽  
pp. 1400
Author(s):  
Marta Bertola ◽  
Andrea Ferrarini ◽  
Giovanna Visioli
Keyword(s):  
Microbial Diversity ◽  
Food Quality ◽  
Plant Biomass ◽  
Soil Microbial Communities ◽  
Well Being ◽  
Plant Health ◽  
Soil Microbiome ◽  
Soil Microbial Diversity ◽  
Soil Biodiversity ◽  
Soil Microbial

Soil is one of the key elements for supporting life on Earth. It delivers multiple ecosystem services, which are provided by soil processes and functions performed by soil biodiversity. In particular, soil microbiome is one of the fundamental components in the sustainment of plant biomass production and plant health. Both targeted and untargeted management of soil microbial communities appear to be promising in the sustainable improvement of food crop yield, its nutritional quality and safety. –Omics approaches, which allow the assessment of microbial phylogenetic diversity and functional information, have increasingly been used in recent years to study changes in soil microbial diversity caused by agronomic practices and environmental factors. The application of these high-throughput technologies to the study of soil microbial diversity, plant health and the quality of derived raw materials will help strengthen the link between soil well-being, food quality, food safety and human health.

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