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.

Impacts of cover crops and nitrogen fertilization on agricultural soil fungal and bacterial communities

2021 ◽  
Author(s):  
Sarah C. Castle ◽  
Deborah A. Samac ◽  
Jessica L. Gutknecht ◽  
Michael J. Sadowsky ◽  
Carl J. Rosen ◽  
...  
Keyword(s):  
Cover Crops ◽  
Nitrogen Fertilization ◽  
Bacterial Communities ◽  
Agricultural Soil

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 Climate Change and Physical Disturbance Manipulations Result in Distinct Biological Soil Crust Communities

2015 ◽  
Vol 81 (21) ◽  
pp. 7448-7459 ◽  
Author(s):  
Blaire Steven ◽  
Cheryl R. Kuske ◽  
La Verne Gallegos-Graves ◽  
Sasha C. Reed ◽  
Jayne Belnap
Keyword(s):  
Climate Change ◽  
Land Use ◽  
Bacterial Communities ◽  
Field Experiments ◽  
Metagenomic Sequencing ◽  
Small Community ◽  
Soil Warming ◽  
Bacterial Composition ◽  
Soil Bacterial ◽  
The Impact

ABSTRACTBiological soil crusts (biocrusts) colonize plant interspaces in many drylands and are critical to soil nutrient cycling. Multiple climate change and land use factors have been shown to detrimentally impact biocrusts on a macroscopic (i.e., visual) scale. However, the impact of these perturbations on the bacterial components of the biocrusts remains poorly understood. We employed multiple long-term field experiments to assess the impacts of chronic physical (foot trampling) and climatic changes (2°C soil warming, altered summer precipitation [wetting], and combined warming and wetting) on biocrust bacterial biomass, composition, and metabolic profile. The biocrust bacterial communities adopted distinct states based on the mechanism of disturbance. Chronic trampling decreased biomass and caused small community compositional changes. Soil warming had little effect on biocrust biomass or composition, while wetting resulted in an increase in the cyanobacterial biomass and altered bacterial composition. Warming combined with wetting dramatically altered bacterial composition and decreasedCyanobacteriaabundance. Shotgun metagenomic sequencing identified four functional gene categories that differed in relative abundance among the manipulations, suggesting that climate and land use changes affected soil bacterial functional potential. This study illustrates that different types of biocrust disturbance damage biocrusts in macroscopically similar ways, but they differentially impact the resident soil bacterial communities, and the communities' functional profiles can differ depending on the disturbance type. Therefore, the nature of the perturbation and the microbial response are important considerations for management and restoration of drylands.

scholarly journals The Core and Seasonal Microbiota of Raw Bovine Milk in Tanker Trucks and the Impact of Transfer to a Milk Processing Facility

mBio ◽  
2016 ◽  
Vol 7 (4) ◽  
Author(s):  
Mary E. Kable ◽  
Yanin Srisengfa ◽  
Miles Laird ◽  
Jose Zaragoza ◽  
Jeremy McLeod ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Dairy Products ◽  
Bovine Milk ◽  
Raw Milk ◽  
High Quality ◽  
Bacterial Composition ◽  
Core Microbiota ◽  
Milk Samples ◽  
Processing Facility ◽  
The Impact

ABSTRACTCurrently, the bacterial composition of raw milk in tanker trucks and the outcomes of transfer and storage of that milk at commercial processing facilities are not well understood. We set out to identify the bacteria in raw milk collected for large-scale dairy product manufacturing. Raw bovine milk samples from 899 tanker trucks arriving at two dairy processors in San Joaquin Valley of California during three seasons (spring, summer, and fall) were analyzed by community 16S rRNA gene sequencing. This analysis revealed highly diverse bacterial populations, which exhibited seasonal differences. Raw milk collected in the spring contained the most diverse bacterial communities, with the highest total cell numbers and highest proportions being those ofActinobacteria. Even with this complexity, a core microbiota was present, consisting of 29 taxonomic groups and high proportions ofStreptococcusandStaphylococcusand unidentified members ofClostridiales. Milk samples were also collected from five large-volume silos and from 13 to 25 tankers whose contents were unloaded into each of them during 2 days in the summer. Transfer of the milk to storage silos resulted in two community types. One group of silos contained a high proportion ofStreptococcusspp. and was similar in that respect to the tankers that filled them. The community found in the other group of silos was distinct and dominated byAcinetobacter. Overall, despite highly diverse tanker milk community structures, distinct milk bacterial communities were selected within the processing facility environment. This knowledge can inform the development of new sanitation procedures and process controls to ensure the consistent production of safe and high-quality dairy products on a global scale.IMPORTANCERaw milk harbors diverse bacteria that are crucial determinants of the quality and safety of fluid milk and (fermented) dairy products. These bacteria enter farm milk during transport, storage, and processing. Although pathogens are destroyed by pasteurization, not all bacteria and their associated enzymes are eliminated. Our comprehensive analyses of the bacterial composition of raw milk upon arrival and shortly after storage at major dairy processors showed that the communities of milk microbiota are highly diverse. Even with these differences, there was a core microbiota that exhibited distinct seasonal trends. Remarkably, the effects of the processing facility outweighed those of the raw milk microbiome and the microbial composition changed distinctly within some but not all silos within a short time after transfer. This knowledge can be used to inform cleaning and sanitation procedures as well as to enable predictions of the microbial communities in raw milk that result in either high-quality or defective products.

scholarly journals The impact of distillery effluent irrigation on plant-growth-promoting traits and taxonomic composition of bacterial communities in agricultural soil

2019 ◽  
Author(s):  
Priyanka Kumari ◽  
Binu M. Tripathi ◽  
Ram N. Singh ◽  
Anil K. Saxena ◽  
Rajeev Kaushik
Keyword(s):  
Plant Growth ◽  
Bacterial Communities ◽  
Agricultural Soil ◽  
Soil Microorganisms ◽  
Taxonomic Composition ◽  
Distillery Effluent ◽  
Pgp Traits ◽  
Plant Growth Promoting ◽  
Growth Promoting ◽  
The Impact

AbstractLong-term irrigation of agricultural fields with distillery effluent (DE) may alter the physical, chemical and biological properties of the soil. Microorganisms are critical to the maintenance of soil health and productivity. However, the impact of DE irrigation on activity and taxonomy of soil microorganisms is poorly understood. Here we studied plant-growth-promoting (PGP) traits and taxonomic composition of bacterial communities in agricultural soil irrigated with DE in conjugation with irrigation water, using cultivation-dependent and - independent methods. Most of the bacterial isolates obtained from DE irrigated soil were found to display PGP traits (phosphate solubilization, siderophore, indolic compounds and ammonia production). Diverse bacterial taxa were found in both culturable bacterial community and 16S rRNA gene clone library, which belonged to bacterial phylaProteobacteria(Alpha-, Beta- and Gamma- subdivisions),Firmicutes, Actinobacteria, Acidobacteria, BacteroidetesandGemmatimonadates. Overall, these results indicate that PGP traits and taxonomic diversity of soil bacterial communities were not severely impacted by DE irrigation.

scholarly journals Larval density affects phenotype and surrounding bacterial community without altering gut microbiota in Drosophila melanogaster

2020 ◽  
Vol 96 (4) ◽  
Author(s):  
Y Henry ◽  
P Tarapacki ◽  
H Colinet
Keyword(s):  
Drosophila Melanogaster ◽  
Uric Acid ◽  
Bacterial Communities ◽  
Larval Density ◽  
Ammonia Concentration ◽  
Stressful Situation ◽  
Bacterial Composition ◽  
Rearing Density ◽  
Larval Crowding ◽  
The Impact

ABSTRACT Larval crowding represents a complex stressful situation arising from inter-individual competition for time- and space-limited resources. The foraging of a large number of individuals may alter the chemical and bacterial composition of food and in turn affect individual's traits. Here we used Drosophila melanogaster to explore these assumptions. First, we used a wide larval density gradient to investigate the impact of crowding on phenotypical traits. We confirmed that high densities increased development time and pupation height, and decreased viability and body mass. Next, we measured concentrations of common metabolic wastes (ammonia, uric acid) and characterized bacterial communities, both in food and in larvae, for three contrasting larval densities (low, medium and high). Ammonia concentration increased in food from medium and high larval densities, but remained low in larvae regardless of the larval density. Uric acid did not accumulate in food but was detected in larvae. Surprisingly, bacterial composition remained stable in guts of larvae whatever their rearing density, although it drastically changed in the food. Overall, these results indicate that crowding deeply affects individuals, and also their abiotic and biotic surroundings. Environmental bacterial communities likely adapt to altered nutritional situations resulting from crowding, putatively acting as scavengers of larval metabolic wastes.

scholarly journals Abiotic environmental factors override phytoplankton succession in shaping both free-living and attached bacterial communities in a highland lake

AMB Express ◽  
2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Huan Wang ◽  
Rong Zhu ◽  
Xiaolin Zhang ◽  
Yun Li ◽  
Leyi Ni ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Bacterial Community ◽  
Species Composition ◽  
Community Composition ◽  
Bacterial Communities ◽  
Phytoplankton Community ◽  
Bacterial Community Composition ◽  
Free Living ◽  
The Impact ◽  
Abiotic Environmental Factors

Abstract Bacterial communities are an important part of biological diversity and biogeochemical cycling in aquatic ecosystems. In this study, the relationship amongst the phytoplankton species composition and abiotic environmental factors on seasonal changes in the community composition of free-living and attached bacteria in Lake Erhai were studied. Using Illumina high-throughput sequencing, we found that the impact of environmental factors on both the free-living and attached bacterial community composition was greater than that of the phytoplankton community, amongst which total phosphorus, Secchi disk, water temperature, dissolved oxygen and conductivity strongly influenced bacterial community composition. Microcystis blooms associated with subdominant Psephonema occurred during the summer and autumn, and Fragilaria, Melosira and Mougeotia were found at high densities in the other seasons. Only small numbers of algal species-specific bacteria, including Xanthomonadaceae (Proteobacteria) and Alcaligenaceae (Betaproteobacteria), were tightly coupled to Microcystis and Psephonema during Microcystis blooms. Redundancy analysis showed that although the composition of the bacterial communities was controlled by species composition mediated by changes in phytoplankton communities and abiotic environmental factors, the impact of the abiotic environment on both free-living and attached bacterial community compositions were greater than the impact of the phytoplankton community. These results suggest that the species composition of both free-living and attached bacterial communities are affected by abiotic environmental factors, even when under strong control by biotic factors, particularly dominant genera of Microcystis and Psephonema during algal blooms.

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 Differing Dietary Nutrients and Diet-associated Bacteria has Limited Impact on Spider Gut Microbiota Composition

2021 ◽  
Author(s):  
Wang Zhang ◽  
Fengjie Liu ◽  
Yang Zhu ◽  
Runhua Han ◽  
Letian Xu ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Bacterial Communities ◽  
Bacterial Flora ◽  
Lasius Niger ◽  
Microbial Composition ◽  
Bacterial Composition ◽  
Associated Bacteria ◽  
Limited Impact ◽  
Dietary Nutrients ◽  
The Impact

Abstract Spiders are a key predator of insects across ecosystems and possess great potential as pest control agents. Unfortunately, it is difficult to artificially cultivate multiple generations of most spider species. Since gut bacterial flora has been shown to significantly alter nutrient availability, it is plausible that the spiders’ microbial community play a key role in their unsuccessful breeding. However, both the gut microbial composition and its influencing factors in many spiders remain a mystery. In this study, the gut microbiota of Campanicola campanulata, specialist prey on ants and are widely distributed across China, was characterized. After, the impact of diet and diet-associated bacteria on gut bacterial composition was evaluated. First, two species of prey ants (Lasius niger and Tetramorium caespitum) were collected from different locations and fed to C. campanulata. For each diet, we then profiled the nutritional content of the ants, as well as the bacterial communities of both the ants and spiders. Results showed that the protein and carbohydrate content varied between the two prey ant species, and that the bacterial communities of the ants were clearly delineated by collection site. However, no significant differences were found in the gut microbiota of spiders that were fed the differing ants. Together, these results indicate that nutritional variation and diet-associated bacterial differences have a limited impact on the microbial composition of spider guts, suggesting that spiders have a mechanism keeping their gut bacterial community stable to ensure normal physiological function and development.

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