Ecotype-Dependent Response of Bacterial Communities Associated with Arabidopsis to Cold Acclimation

Low temperature is a primary factor limiting geographical distribution of plants and crop yield in large areas of the world. Plant-associated microbial communities have rarely been acknowledged as possible determinants of cold acclimation, the process leading to freezing tolerance in plants. Here we studied the impact of cold acclimation on leaf-associated bacteria by analyzing 10 different Arabidopsis ecotypes differing widely in their freezing tolerance. In climate chamber experiments, we found that leaves of all Arabidopsis accessions were colonized by highly diverse bacterial taxa (852 operational taxonomic units) mainly from Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. During cold acclimation, in all ecotypes the bacterial community composition and diversity, and especially the core species composition changed drastically. However, the response of the bacterial communities was highly ecotype-dependent; sensitive and tolerant accessions shared only eight responders. Unique responders in tolerant accessions were identified as putative indicators of freezing tolerance. Thus, leaf bacteria appear to be genotype-dependent associated with cold acclimation, which suggests an additional function of plant−microbe interaction and may open new possibilities for biotechnological applications.

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Dietary and Developmental Shifts in Butterfly-Associated Bacterial Communities

10.1101/196816 ◽

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.

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

10.21203/rs.2.16025/v1 ◽

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.

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Autumn Warming Delays the Downregulation of Photosynthesis and Does Not Increase the Risk of Freezing Damage in Interior and Coastal Douglas-fir

Frontiers in Forests and Global Change ◽

10.3389/ffgc.2021.688534 ◽

2021 ◽

Vol 4 ◽

Author(s):

Devin Noordermeer ◽

Vera Marjorie Elauria Velasco ◽

Ingo Ensminger

Keyword(s):

Cold Acclimation ◽

Freezing Tolerance ◽

Xanthophyll Cycle ◽

Low Temperatures ◽

Cold Hardiness ◽

Photosynthetic Activity ◽

Elevated Temperatures ◽

Douglas Fir ◽

The Impact ◽

Xanthophyll Cycle Pigment

During autumn, evergreen conifers utilize the decrease in daylength and temperature as environmental signals to trigger cold acclimation, a process that involves the downregulation of photosynthesis, upregulation of photoprotection, and development of cold hardiness. Global warming will delay the occurrence of autumn low temperatures while daylength remains unaffected. The impact of autumn warming on cold acclimation and the length of the carbon uptake period of species with ranges that encompass diverse climates, such as Douglas-fir (Pseudotsuga menziesii), remains unclear. Our study investigated intraspecific variation in the effects of autumn warming on photosynthetic activity, photosynthetic pigments, and freezing tolerance in two interior (var. glauca) and two coastal (var. menziesii) Douglas-fir provenances. Following growth under simulated summer conditions with long days (16 h photoperiod) and summer temperatures (22/13°C day/night), Douglas-fir seedlings were acclimated to simulated autumn conditions with short days (8 h photoperiod) and either low temperatures (cool autumn, CA; 4/−4°C day/night) or elevated temperatures (warm autumn, WA; 19/11°C day/night). Exposure to low temperatures in the CA treatment induced the downregulation of photosynthetic carbon assimilation and photosystem II efficiency, increased the size and de-epoxidation of the xanthophyll cycle pigment pool, and caused the development of sustained nonphotochemical quenching (NPQ). Seedlings in the WA treatment exhibited no downregulation of photosynthesis, no change in xanthophyll cycle pigment de-epoxidation, and no development of sustained NPQ. Albeit these changes, freezing tolerance was not impaired under WA conditions compared with CA conditions. Interior Douglas-fir seedlings developed greater freezing tolerance than coastal seedlings. Our findings suggest that autumn warming, i.e., short photoperiod alone, does not induce the downregulation of photosynthesis in Douglas-fir. Although autumn warming delays the downregulation of photosynthesis, the prolonged period of photosynthetic activity does not bear a trade-off of impaired freezing tolerance.

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Impact of Virioplankton on Archaeal and Bacterial Community Richness as Assessed in Seawater Batch Cultures

Applied and Environmental Microbiology ◽

10.1128/aem.70.2.804-813.2004 ◽

2004 ◽

Vol 70 (2) ◽

pp. 804-813 ◽

Cited By ~ 75

Author(s):

Christian Winter ◽

Arjan Smit ◽

Gerhard J. Herndl ◽

Markus G. Weinbauer

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Rflp Analysis ◽

Rrna Gene ◽

Tropical Atlantic ◽

Viral Lysis ◽

Batch Cultures ◽

Operational Taxonomic Units ◽

The Impact

ABSTRACT During cruises in the tropical Atlantic Ocean (January to February 2000) and the southern North Sea (December 2000), experiments were conducted to monitor the impact of virioplankton on archaeal and bacterial community richness. Prokaryotic cells equivalent to 10 to 100% of the in situ abundance were inoculated into virus-free seawater, and viruses equivalent to 35 to 360% of the in situ abundance were added. Batch cultures with microwave-inactivated viruses and without viruses served as controls. The apparent richness of archaeal and bacterial communities was determined by terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified 16S rRNA gene fragments. Although the estimated richness of the prokaryotic communities generally was greatly reduced within the first 24 h of incubation due to confinement, the effects of virus amendment were detected at the level of individual operational taxonomic units (OTUs) in the T-RFLP patterns of both groups, Archaea and Bacteria. One group of OTUs was detected in the control samples but was absent from the virus-treated samples. This negative response of OTUs to virus amendment probably was caused by viral lysis. Additionally, we found OTUs not responding to the amendments, and several OTUs exhibited variable responses to the addition of inactive or active viruses. Therefore, we conclude that individual members of pelagic archaeal and bacterial communities can be differently affected by the presence of virioplankton.

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Fecal Bacterial Community of Allopatric Przewalski’s Gazelles and Their Sympatric Relatives

Frontiers in Microbiology ◽

10.3389/fmicb.2021.737042 ◽

2021 ◽

Vol 12 ◽

Author(s):

Ruoshuang Liu ◽

Jianbin Shi ◽

Susanne Shultz ◽

Dongsheng Guo ◽

Dingzhen Liu

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Bacterial Communities ◽

Bacterial Community Composition ◽

Ecological Factors ◽

Ovis Aries ◽

Host Community ◽

Tibetan Sheep ◽

Fecal Bacterial Community ◽

The Impact

Mammal gastrointestinal tracts harbor diverse bacterial communities that play important roles in digestion, development, behavior, and immune function. Although, there is an increasing understanding of the factors that affect microbial community composition in laboratory populations, the impact of environment and host community composition on microbiomes in wild populations is less understood. Given that the composition of bacterial communities can be shaped by ecological factors, particularly exposure to the microbiome of other individuals, inter-specific interactions should impact on microbiome community composition. Here, we evaluated inter-population and inter-specific similarity in the fecal microbiota of Przewalski’s gazelle (Procapra przewalskii), an endangered endemic ruminant around Qinghai Lake in China. We compared the fecal bacterial communities of three Przewalski’s gazelle populations, with those of two sympatric ruminants, Tibetan gazelle (Procapra picticaudata) and Tibetan sheep (Ovis aries). The fecal bacterial community richness (Chao1, ACE) did not vary across the three Przewalski’s gazelle populations, nor did the composition vary between species. In contrast, the managed Przewalski’s gazelle population had higher bacterial diversity (Shannon and Simpson) and was more similar to its sympatric Tibetan sheep in beta diversity than the wild Przewalski’s gazelle populations. These results suggest that ecological factors like host community composition or diet affect Przewalski’s gazelle’s gastrointestinal bacterial community. The role of bacterial community composition in maintaining gastrointestinal health should be assessed to improve conservation management of endangered Przewalski’s gazelle. More broadly, captive breeding and reintroduction efforts may be impeded, where captive management results in dysbiosis and introduction of pathogenic bacteria. In free ranging populations, where wildlife and livestock co-occur, infection by domestic pathogens and diseases may be an underappreciated threat to wild animals.

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Groundwater bacterial communities evolve over time, exhibiting oscillating similarity patterns in response to recharge

10.1101/2021.03.18.434713 ◽

2021 ◽

Author(s):

Lijuan Yan ◽

Syrie Hermans ◽

Kai Uwe Totsche ◽

Robert Lehmann ◽

Martina Herrmann ◽

...

Keyword(s):

Groundwater Recharge ◽

Bacterial Communities ◽

Bacterial Community Composition ◽

High Temporal Resolution ◽

Aquatic Environments ◽

Rrna Gene ◽

Sequencing Data ◽

Environmental Selection ◽

The Impact ◽

Over Time

Time series analyses are a crucial tool for uncovering the patterns and processes shaping microbial communities and their functions, especially in aquatic ecosystems. Subsurface aquatic environments are perceived to be more stable than oceans and lakes, due to the lack of sunlight, the absence of photosysnthetically-driven primary production, low temperature variations, and oligotrophic conditions. However, periodic groundwater recharge should affect the structure and succession of groundwater microbiomes. To disentangle the long-term temporal changes in groundwater bacterial communities of shallow fractured bedrock community, and identify the drivers of the observed patterns, we analysed bacterial 16S rRNA gene sequencing data for samples collected monthly from three groundwater wells over a six-year period (n=230) along a hillslope recharge area. We show that the bacterial communities in the groundwater of limestone-mudstone alternations were not stable over time and showed oscillating dissimilarity patterns which corresponded to periods of groundwater recharge; the impact of recharge events on the groundwater microbiome was linked to the recharge strength and local environmental selection strength. Sampling period was able to explain up to 29.5% of the variability in bacterial community composition. We observed an increase in dissimilarity over time (generalized additive model P < 0.001) indicating that the successive recharge events result in communities that are increasingly more dissimilar to the initial reference time point. The majority of groundwater bacteria originated from the recharge-related sources (mean = 66.5%, SD = 15.1%) and specific bacterial taxa were identified as being either enriched or repressed during recharge events. Overall, similar to surface aquatic environments, groundwater microbiomes vary through time, though we revealed groundwater recharges as unique driving factors for these patterns. The high temporal resolution employed here highlights the complex dynamics of bacterial communities in groundwater and demonstrated that successive shocks disturb the bacterial communities, leading to decreased similarity to the initial state over time.

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Linkages of Soil Nutrients and Diazotrophic Microbiome under Sugarcane-Legume Intercropping

10.20944/preprints201810.0382.v1 ◽

2018 ◽

Author(s):

Manoj Kumar Solanki ◽

Chang-Ning Li ◽

Fei-Yong Wang ◽

Zhen Wang ◽

Tao-Ju Lan ◽

...

Keyword(s):

Soil Fertility ◽

Soil Properties ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Nifh Gene ◽

Cultivation Systems ◽

Operational Taxonomic Units ◽

Land Use Efficiency ◽

Alpha Proteobacteria ◽

The Impact

Intercropping significantly improves land use efficiency and soil fertility. This study examines the impact of three cultivation systems (monoculture sugarcane, peanut-sugarcane and soybean-sugarcane intercropping) on soil properties and diazotrophs. Sugarcane rhizosphere soil was sampled from the farmers’ field. Soil properties and nifH gene abundance were analyzed by high throughput sequencing. Moreover, a total of 436,458 nifH gene sequences were obtained and classified into the 3201 unique operational taxonomic units (OTUs). Maximum unique OTUs resulted with soybean-sugarcane intercropping (<375). The dominant groups across all cultivation were Alpha-proteobacteria and Beta-proteobacteria. On the basis of microbial community structure, intercropping systems were more diverse than monoculture sugarcane. In the genus level, Bradyrhizobium, Burkholderia, Pelomonas, and Sphingomonas were predominant in the intercropping systems. Moreover, diazotrophic bacterial communities of these cultivation systems were positively correlated to the soil pH and soil enzyme protease. Moreover, low available P recovered from intercropping system showed a strong correlation with higher nutrient uptake activity of soil microbes. Based on the results, our investigation concluded that intercropping system caused a positive effect on the growth of diazotrophic bacterial communities and it might boost the soil fertility and this kind of study helps to develop an eco-friendly technology for sustainable sugarcane production.

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Environmental characteristics and changes of bacterial communities in the meltwater runoff of glacier in Ny-Alesund, Arctic

10.21203/rs.3.rs-906889/v1 ◽

2021 ◽

Author(s):

Lidong Lin ◽

Nengfei Wang ◽

Wenbing Han ◽

Botao Zhang ◽

Jiaye Zang ◽

...

Keyword(s):

Bacterial Community ◽

Bacterial Diversity ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Bacterial Community Composition ◽

Operational Taxonomic Units ◽

The Core ◽

Meltwater Runoff ◽

Glacial Runoff ◽

Weighted Correlation

Abstract The present study assessed the diversity and composition of bacterial communities in glacial runoff and glacial soils in the Midre Lovénbreen glacier region of Svalbard. A total of 6,593 operational taxonomic units were identified by high-throughput sequencing. The results showed differences in bacterial community composition between the upper and lower reaches of glacial runoff. The abundance of Actinobacteria, Firmicutes, Betaproteobacteria and Gammaproteobacteria in the upper reaches of glacial runoff was higher than that in the lower reaches. In contrast, the the abundance of Cyanobacteria and Alphaproteobacteria in the downstream of glacial runoff was higher than that in the upstream. In addition, we compared bacterial diversity and composition between glacial runoff areas and soils. The chart analysis showed that bacterial diversity in glacial soil was higher than that in the glacial runoff. Some typical bacteria in the soil, such as Actinobacteria, entered glacial runoff through contact between them. The abundance of Acidobacteria, Sphingobacterium and Flavobacterium was higher in glacial soil. Weighted correlation network analysis showed that the core bacteria in glacial runoff and glacial soil were typical bacteria in different habitats. Distance-based redundancy analysis revealed that NO 2 - -N was the most significant factor affecting the distribution of soil bacterial community, while NO 3 - -N was the most significant factor affecting the distribution of glacial runoff bacterial community.

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Bacterial Operational Taxonomic Units Replace the Interactive Roles of Other Operational Taxonomic Units Under Strong Environmental Changes

Current Genomics ◽

10.2174/1389202921999200716104355 ◽

2020 ◽

Vol 21 (7) ◽

pp. 512-524

Author(s):

Rajiv Das Kangabam ◽

Yumnam Silla ◽

Gunajit Goswami ◽

Madhumita Barooah

Keyword(s):

Land Use ◽

Aquatic Ecosystem ◽

Bacterial Community Composition ◽

Winter Season ◽

Soil Samples ◽

Metagenomic Dna ◽

Operational Taxonomic Units ◽

Loktak Lake ◽

Post Monsoon ◽

The Impact

Background: Microorganisms are an important component of an aquatic ecosystem and play a critical role in the biogeochemical cycle which influences the circulation of the materials and maintains the balance in aquatic ecosystems. Objective: The seasonal variation along with the impact of anthropogenic activities, water quality, bacterial community composition and dynamics in the Loktak Lake, the largest freshwater lake of North East India, located in the Indo-Burma hotspot region was assessed during post-monsoon and winter season through metagenome analysis. Methods: Five soil samples were collected during Post-monsoon and winter season from the Loktak Lake that had undergone different anthropogenic impacts. The metagenomic DNA of the soil samples was extracted using commercial metagenomic DNA extraction kits following the manufacturer’s instruction. The extracted DNA was used to prepare the NGS library and sequenced in the Illumina MiSeq platform. Results: Metagenomics analysis reveals Proteobacteria as the predominant community followed by Acidobacteria and Actinobacteria. The presence of these groups of bacteria indicates nitrogen fixation, oxidation of iron, sulfur, methane, and source of novel antibiotic candidates. The bacterial members belonging to different groups were involved in various biogeochemical processes, including fixation of carbon and nitrogen, producing streptomycin, gramicidin and perform oxidation of sulfur, sulfide, ammonia, and methane. Conclusion: The outcome of this study provides a valuable dataset representing a seasonal profile across various land use and analysis, targeting at establishing an understanding of how the microbial communities vary across the land use and the role of keystone taxa. The findings may contribute to searches for microbial bio-indicators as biodiversity markers for improving the aquatic ecosystem of the Loktak Lake.

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Bacterial communities associated with individual transparent exopolymer particles (TEP)

Journal of Plankton Research ◽

10.1093/plankt/fbz022 ◽

2019 ◽

Vol 41 (4) ◽

pp. 561-565 ◽

Cited By ~ 7

Author(s):

Birthe Zäncker ◽

Anja Engel ◽

Michael Cunliffe

Keyword(s):

Organic Matter ◽

Bacterial Community ◽

Dna Sequencing ◽

Bacterial Communities ◽

Bacterial Community Composition ◽

Euphotic Zone ◽

Carbon Export ◽

Transparent Exopolymer Particles ◽

Operational Taxonomic Units ◽

Insight Into

Abstract Transparent exopolymer particles (TEP) are polysaccharide-rich microgels that are prevalent in the marine environment and have important roles in the aggregation of organic matter and carbon export from the euphotic zone. TEP are readily colonized by bacteria and utilized by specialized taxa, such as Alteromonadaceae. However, bacterial community composition specifically attached to natural TEP remains largely unknown. In this study, we isolated individual TEP from Plymouth Sound (UK) and performed DNA sequencing of the TEP-attached bacterial communities. We also sampled the cognate bulk seawater total bacterial communities for comparison. The bacterial communities associated with individual TEP showed distinct differences compared to the total bulk bacterioplankton communities, with Alteromonadaceae significantly more abundant on TEP. The TEP-associated Alteromonadaceae consisted of two operational taxonomic units that were closely related to Marinobacter and Glaciecola, both previously associated with biogenic aggregates and microgel-rich habitats. This study provides novel insight into marine bacterial–microgel interactions.

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