scholarly journals H2-saturation of high affinity H2-oxidizing bacteria alters the ecological niche of soil microorganisms unevenly among taxonomic groups

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1782 ◽  
Author(s):  
Sarah Piché-Choquette ◽  
Julien Tremblay ◽  
Susannah G. Tringe ◽  
Philippe Constant
Keyword(s):  
Bacterial Communities ◽  
Soil Microbial Communities ◽  
Oxidation Activity ◽  
Soil Microbial ◽  
High Affinity ◽  
Correlation Networks ◽  
Soil Bacterial Community Structure ◽  
Microbe Interactions ◽  
Taxonomic Groups ◽  
The Impact

Soil microbial communities are continuously exposed to H2diffusing into the soil from the atmosphere. N2-fixing nodules represent a peculiar microniche in soil where H2can reach concentrations up to 20,000 fold higher than in the global atmosphere (0.530 ppmv). In this study, we investigated the impact of H2exposure on soil bacterial community structure using dynamic microcosm chambers simulating soil H2exposure from the atmosphere and N2-fixing nodules. Biphasic kinetic parameters governing H2oxidation activity in soil changed drastically upon elevated H2exposure, corresponding to a slight but significant decay of high affinity H2-oxidizing bacteria population, accompanied by an enrichment or activation of microorganisms displaying low-affinity for H2. In contrast to previous studies that unveiled limited response by a few species, the relative abundance of 958 bacterial ribotypes distributed among various taxonomic groups, rather than a few distinct taxa, was influenced by H2exposure. Furthermore, correlation networks showed important alterations of ribotype covariation in response to H2exposure, suggesting that H2affects microbe-microbe interactions in soil. Taken together, our results demonstrate that H2-rich environments exert a direct influence on soil H2-oxidizing bacteria in addition to indirect effects on other members of the bacterial communities.

scholarly journals Microbial Inoculants and Their Impact on Soil Microbial Communities: A Review

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Darine Trabelsi ◽  
Ridha Mhamdi
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Future Research ◽  
Bacterial Strains ◽  
Microbial Inoculants ◽  
Soil Microbial ◽  
Functional Capabilities ◽  
Plant Soil ◽  
Taxonomic Groups ◽  
The Impact

The knowledge of the survival of inoculated fungal and bacterial strains in field and the effects of their release on the indigenous microbial communities has been of great interest since the practical use of selected natural or genetically modified microorganisms has been developed. Soil inoculation or seed bacterization may lead to changes in the structure of the indigenous microbial communities, which is important with regard to the safety of introduction of microbes into the environment. Many reports indicate that application of microbial inoculants can influence, at least temporarily, the resident microbial communities. However, the major concern remains regarding how the impact on taxonomic groups can be related to effects on functional capabilities of the soil microbial communities. These changes could be the result of direct effects resulting from trophic competitions and antagonistic/synergic interactions with the resident microbial populations, or indirect effects mediated by enhanced root growth and exudation. Combination of inoculants will not necessarily produce an additive or synergic effect, but rather a competitive process. The extent of the inoculation impact on the subsequent crops in relation to the buffering capacity of the plant-soil-biota is still not well documented and should be the focus of future research.

The impact of nanoscale zero-valent iron particles on soil microbial communities is soil dependent

2019 ◽  
Vol 364 ◽  
pp. 591-599 ◽  
Author(s):  
María T. Gómez-Sagasti ◽  
Lur Epelde ◽  
Mikel Anza ◽  
Julen Urra ◽  
Itziar Alkorta ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Zero Valent Iron ◽  
Iron Particles ◽  
Soil Microbial ◽  
Nanoscale Zero Valent Iron ◽  
The Impact

scholarly journals Biocrust-forming mosses mitigate the impact of aridity on soil microbial communities in drylands: observational evidence from three continents

2018 ◽  
Vol 220 (3) ◽  
pp. 824-835 ◽  
Author(s):  
Manuel Delgado-Baquerizo ◽  
Fernando T. Maestre ◽  
David J. Eldridge ◽  
Matthew A. Bowker ◽  
Thomas C. Jeffries ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Observational Evidence ◽  
Soil Microbial ◽  
The Impact

scholarly journals Depression of Groundwater Table and Reduced Nitrogen Application Jointly Regulate the Bacterial Composition of nirS-Type and nirK-Type Genes in Agricultural Soil

Water ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 3459
Author(s):  
Fangfang Bai ◽  
Xuebin Qi ◽  
Ping Li ◽  
Dongmei Qiao ◽  
Jianming Wang ◽  
...  
Keyword(s):  
Species Composition ◽  
Nitrogen Fertilization ◽  
Bacterial Communities ◽  
Agricultural Soil ◽  
Soil Microbial Communities ◽  
Groundwater Table ◽  
Nitrogen Application ◽  
Bacterial Composition ◽  
Reduced Nitrogen ◽  
The Impact

Despite the known influence of nitrogen fertilization and groundwater conditions on soil microbial communities, the effects of their interactions on bacterial composition of denitrifier communities have been rarely quantified. Therefore, a large lysimeter experiment was conducted to examine how and to what extent groundwater table changes and reduced nitrogen application would influence the bacterial composition of nirK-type and nirS-type genes. The bacterial composition of nirK-type and nirS-type genes were compared at two levels of N input and three groundwater table levels. Our results demonstrated that depression of groundwater table, reduced nitrogen application and their interactions would lead to drastic shifts in the bacterial composition of nirS-type and nirK-type genes. Structural equation models (SEMs) indicated that depression of groundwater table and reduced nitrogen application not only directly altered the species composition of denitrifier bacterial communities, but also indirectly influenced them through regulating soil nutrient and salinity. Furthermore, the variation in soil NO3−–N and electrical conductivity caused by depression of groundwater table and reduced nitrogen application played the most important role in altering the community composition of denitrifier bacterial communities. Together, our findings provide first-hand evidence that depression of groundwater table and reduced nitrogen application jointly regulate the species composition of denitrifier bacterial communities in agricultural soil. We highlight that local environmental conditions such as groundwater table and soil attributes should be taken into account to enrich our knowledge of the impact of nitrogen fertilization on soil denitrifier bacterial communities, or even biogeochemical cycles.

scholarly journals Soil Heating at High Temperatures and Different Water Content: Effects on the Soil Microorganisms

Geosciences ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 355
Author(s):  
Ana Barreiro ◽  
Alba Lombao ◽  
Angela Martín ◽  
Javier Cancelo-González ◽  
Tarsy Carballas ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Water Content ◽  
Thermal Shock ◽  
Soil Microbial Communities ◽  
Initial Water Content ◽  
Initial Water ◽  
Soil Heating ◽  
Soil Microbial ◽  
Induced Changes ◽  
The Impact

Soil properties determining the thermal transmissivity, the heat duration and temperatures reached during soil heating are key factors driving the fire-induced changes in soil microbial communities. The aim of the present study is to analyze, under laboratory conditions, the impact of the thermal shock (infrared lamps reaching temperatures of 100 °C, 200 °C and 400 °C) and moisture level (0%, 25% and 50% per soil volume) on the microbial properties of three soil mixtures from different sites. The results demonstrated that the initial water content was a determinant factor in the response of the microbial communities to soil heating treatments. Measures of fire impact included intensity and severity (temperature, duration), using the degree-hours method. Heating temperatures produced varying thermal shock and impacts on biomass, bacterial activity and microbial community structure.

scholarly journals Soil Microbial Community Structure and Physicochemical Properties in Amomum tsaoko-based Agroforestry Systems in the Gaoligong Mountains, Southwest China

2019 ◽  
Vol 11 (2) ◽  
pp. 546 ◽  
Author(s):  
Guizhou Liu ◽  
Man Jin ◽  
Chuantao Cai ◽  
Chaonan Ma ◽  
Zhongsuzhi Chen ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Biomass ◽  
Physicochemical Properties ◽  
Phospholipid Fatty Acid ◽  
Soil Microbial Communities ◽  
Total Carbon ◽  
Native Forest ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
The Impact

Amomum tsaoko is cultivated in forests of tropical and subtropical regions of China, and the planting area is expanding gradually. However, little attention has been paid to the impact of A. tsaoko cultivation on the soil characteristics of the regions. We analyzed the effects of the A. tsaoko-forest agroforestry system (AFs) on the composition of soil microbial communities with increasing stand ages. We also compared the soil physicochemical properties, microbial biomass, and phospholipid fatty acid (PLFA) composition between native forest (NF) and AFs. The results showed that the level of total carbon, nitrogen, and organic matter dramatically dropped in AFs with increasing stand ages. pH affected other soil properties and showed close correlation to total carbon (P = 0.0057), total nitrogen (P = 0.0146), organic matter (P = 0.0075), hydrolyzable nitrogen (P = 0.0085), available phosphorus (P < 0.0001), and available potassium (P = 0.0031). PLFAs of bacteria (F = 4.650, P = 0.037), gram-positive bacteria (F = 6.640, P = 0.015), anaerobe (F = 5.672, P = 0.022), and total PLFA (F = 4.349, P = 0.043) were significantly affected by different treatments, with the greatest value for NF treatment, and least value for AF5. However, the microbial biomass declined during the initial 5 years of cultivation, but it reached the previous level after more than 10 years of cultivation. Our research suggests that AFs is a profitable land-use practice in the Gaoligong Mountains and that AFs showed a recovering trend of the soil nutrient condition with increasing stand ages. However, the severe loss of nitrogen in the soil of AFs requires additional nitrogen during cultivation to restore it to pre-cultivation levels.

scholarly journals The relative importance of rapid evolution for plant-microbe interactions depends on ecological context

2014 ◽  
Vol 281 (1785) ◽  
pp. 20140028 ◽  
Author(s):  
Casey P. terHorst ◽  
Jay T. Lennon ◽  
Jennifer A. Lau
Keyword(s):  
Microbial Communities ◽  
Bacterial Abundance ◽  
Rapid Evolution ◽  
Soil Microbial Communities ◽  
Ecological Effect ◽  
Ecological Context ◽  
Ecological Processes ◽  
Soil Microbial ◽  
Long Term Experiment ◽  
Microbe Interactions

Evolution can occur on ecological time-scales, affecting community and ecosystem processes. However, the importance of evolutionary change relative to ecological processes remains largely unknown. Here, we analyse data from a long-term experiment in which we allowed plant populations to evolve for three generations in dry or wet soils and used a reciprocal transplant to compare the ecological effect of drought and the effect of plant evolutionary responses to drought on soil microbial communities and nutrient availability. Plants that evolved under drought tended to support higher bacterial and fungal richness, and increased fungal : bacterial ratios in the soil. Overall, the magnitudes of ecological and evolutionary effects on microbial communities were similar; however, the strength and direction of these effects depended on the context in which they were measured. For example, plants that evolved in dry environments increased bacterial abundance in dry contemporary environments, but decreased bacterial abundance in wet contemporary environments. Our results suggest that interactions between recent evolutionary history and ecological context affect both the direction and magnitude of plant effects on soil microbes. Consequently, an eco-evolutionary perspective is required to fully understand plant–microbe interactions.

scholarly journals Dietary and Developmental Shifts in Butterfly-Associated Bacterial Communities

2017 ◽  
Author(s):  
Kruttika Phalnikar ◽  
Krushnamegh Kunte ◽  
Deepa Agashe
Keyword(s):  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Amplicon Sequencing ◽  
Butterfly Species ◽  
Species Identity ◽  
Active Selection ◽  
Key Factor ◽  
Host Diet ◽  
Taxonomic Groups ◽  
The Impact

ABSTRACTBacterial communities associated with insects can substantially influence host ecology, evolution and behavior. Host diet is a key factor that shapes bacterial communities, but the impact of dietary transitions across insect development is poorly understood. We analyzed bacterial communities of 12 butterfly species across different development stages, using 16S rDNA amplicon sequencing. Butterfly larvae typically consume leaves of a single host plant, whereas adults are more generalist nectar feeders. Thus, we expected bacterial communities to vary substantially across butterfly development. Surprisingly, very few species showed significant developmental transitions in bacterial communities, suggesting weak impacts of dietary transitions across butterfly development. On the other hand, bacterial communities were strongly influenced by butterfly species identity and dietary variation across species. Larvae of most butterfly species largely mirrored bacterial community composition of their diets, suggesting passive acquisition rather than active selection. Overall, our results suggest that although butterflies harbor distinct microbiomes across taxonomic groups and dietary guilds, the dramatic dietary shifts that occur during development do not impose strong selection to maintain distinct bacterial communities.

scholarly journals Effects of shade stress on morphophysiology and rhizosphere soil bacterial communities of two contrasting shade-tolerant turfgrasses

2019 ◽  
Author(s):  
Juanjuan Fu ◽  
Yilan Luo ◽  
Pengyue Sun ◽  
Jinzhu Gao ◽  
Donghao Zhao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Plant Growth ◽  
Bacterial Communities ◽  
Shade Tolerance ◽  
Rhizosphere Soil ◽  
Photosynthetic Capacity ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Soil Bacterial ◽  
The Impact

Abstract Background: Shade presents one of the major abiotic limitations for turfgrass growth. Shade influences plant growth and alters plant metabolism, yet little is known about how shade affects the structure of rhizosphere soil microbial communities and the role of soil microorganisms in plant shade responses. In this study, a glasshouse experiment was conducted to examine the impact of shade stress on the growth and photosynthetic capacity of two contrasting shade-tolerant turfgrasses, shade-tolerant dwarf lilyturf (Ophiopogon japonicus, OJ) and shade-intolerant perennial turf-type ryegrass (Lolium perenne, LP). We also examined soil-plant feedback effects on shade tolerance in the two turfgrass genotypes. Bacterial community composition was assayed using high-throughput sequencing. Results: Our physiochemical data showed that under shade stress, OJ maintained higher photosynthetic capacity and root growth, thus OJ was found to be more shade-tolerant than LP. Shade-intolerant LP responded better to both shade and soil microbes than shade-tolerant OJ. Shade and live soil decreased LP growth but increased biomass allocation to shoots in the live soil. The plant shade response index of LP is higher in the live soil than sterile soil, driven by weakened soil-plant feedback under shade stress. In contrast, there was no difference in these values for OJ under similar shade and soil treatments. Illumina sequencing data revealed that shade stress had little impact on the diversity of the OJ and LP’s bacterial communities, but instead impacted the composition of bacterial communities. The bacterial communities were mostly composed of Proteobacteria and Acidobacteria in OJ soil. Further pairwise fitting analysis showed that a positive correlation of shade-tolerance in two turfgrasses and their bacterial community compositions. Several soil properties (NO3--N, NH4+-N, AK) showed a tight coupling with several major bacterial communities under shade stress, indicating that they are important drivers determining bacterial community structures. Moreover, OJ shared core bacterial taxa known to promote plant growth and confer tolerance to shade stress, which suggests common principles underpinning OJ-microbe interactions. Conclusion: Plant shade tolerance is mediated by soil-plant feedback and shade-induced changes in rhizosphere soil bacterial community structure in OJ and LP plants.

scholarly journals Activation of the SA-Associated Plant Defense Pathway Alters the Composition of Soil Bacterial Communities

2021 ◽  
Author(s):  
Jing Zhang ◽  
Peter G.L. Klinkhamer ◽  
Klaas Vrieling ◽  
T. Martijn Bezemer
Keyword(s):  
Plant Growth ◽  
Microbial Communities ◽  
Signaling Pathway ◽  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
Soil Microbial Communities ◽  
Core Microbiome ◽  
Soil Microbial ◽  
Soil Bacterial ◽  
Sa Signaling

Abstract Background and aimsMany plant species grow better in sterilized than in live soil. Foliar application of SA mitigates this negative effect of live soil on the growth of the plant Jacobaea vulgaris. To examine what causes the positive effect of SA application on plant growth in live soils, we analyzed the effects of SA application on the composition of active rhizosphere bacteria in the live soil. Methods We studied this over four consecutive plant cycles (generations), using mRNA sequencing of the microbial communities in the rhizosphere of J. vulgaris. ResultsOur study shows that the composition of the rhizosphere bacterial communities of J. vulgaris greatly differed among generations. Application of SA resulted in both increases and decreases in a number of active bacterial genera in the rhizosphere soil, but the genera that were affected by the treatment differed among generations. In the first generation, there were no genera that were significantly affected by the SA treatment, indicating that induction of the SA defense pathway in plants does not lead to immediate changes in the soil microbial community. 89 species out of the total 270 (32.4%) were present in all generations in all soils of SA-treated and control plants suggesting that these make up the “core” microbiome. On average in each generation, 72.9% of all genera were present in both soils. Application of SA to plants significantly up-regulated genera of Caballeronia, unclassified Cytophagaceae, Crinalium and Candidatus Thermofonsia Clade 2, and down-regulated genera of Thermomicrobiales, unclassified Rhodobacterales, Paracoccus and Flavihumibacter. While the functions of many of these bacteria are poorly understood, bacteria of the genus Caballeronia play an important role in fixing nitrogen and promoting plant growth, and hence this suggests that activation of the SA signaling pathway in J. vulgaris plants may select for bacterial genera that are beneficial to the plant. ConclusionsOverall, our study shows that aboveground activation of defenses in the plant affects soil microbial communities and, as soil microbes can greatly influence plant performance, this implies that induction of plant defenses can lead to complex above-belowground feedbacks. Further studies should examine how activation of the SA signaling pathway in the plant changes the functional genes of the rhizosphere soil bacterial community.

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