Epichloë Fungal Endophytes Influence Seed-Associated Bacterial Communities

Seeds commonly harbour diverse bacterial communities that can enhance the fitness of future plants. The bacterial microbiota associated with mother plant’s foliar tissues is one of the main sources of bacteria for seeds. Therefore, any ecological factor influencing the mother plant’s microbiota may also affect the diversity of the seed’s bacterial community. Grasses form associations with beneficial vertically transmitted fungal endophytes of genus Epichloë. The interaction of plants with Epichloë endophytes and insect herbivores can influence the plant foliar microbiota. However, it is unknown whether these interactions (alone or in concert) can affect the assembly of bacterial communities in the produced seed. We subjected Lolium multiflorum plants with and without its common endophyte Epichloë occultans (E+, E-, respectively) to an herbivory treatment with Rhopalosiphum padi aphids and assessed the diversity and composition of the bacterial communities in the produced seed. The presence of Epichloë endophytes influenced the seed bacterial microbiota by increasing the diversity and affecting the composition of the communities. The relative abundances of the bacterial taxa were more similarly distributed in communities associated with E+ than E- seeds with the latter being dominated by just a few bacterial groups. Contrary to our expectations, seed bacterial communities were not affected by the aphid herbivory experienced by mother plants. We speculate that the enhanced seed/seedling performance documented for Epichloë-host associations may be explained, at least in part, by the Epichloë-mediated increment in the seed-bacterial diversity, and that this phenomenon may be applicable to other plant-endophyte associations.

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Bacterial diversity and predicted enzymatic function in a multipurpose surface water system – from wastewater effluent discharges to drinking water production

Environmental Microbiome ◽

10.1186/s40793-021-00379-w ◽

2021 ◽

Vol 16 (1) ◽

Author(s):

Ananda Tiwari ◽

Anna-Maria Hokajärvi ◽

Jorge Santo Domingo ◽

Michael Elk ◽

Balamuralikrishna Jayaprakash ◽

...

Keyword(s):

Drinking Water ◽

Surface Water ◽

Bacterial Community ◽

Human Health ◽

Bacterial Diversity ◽

Water Samples ◽

Bacterial Communities ◽

Treatment Process ◽

Pollution Sources ◽

Production Well

Abstract Background Rivers and lakes are used for multiple purposes such as for drinking water (DW) production, recreation, and as recipients of wastewater from various sources. The deterioration of surface water quality with wastewater is well-known, but less is known about the bacterial community dynamics in the affected surface waters. Understanding the bacterial community characteristics —from the source of contamination, through the watershed to the DW production process—may help safeguard human health and the environment. Results The spatial and seasonal dynamics of bacterial communities, their predicted functions, and potential health-related bacterial (PHRB) reads within the Kokemäenjoki River watershed in southwest Finland were analyzed with the 16S rRNA-gene amplicon sequencing method. Water samples were collected from various sampling points of the watershed, from its major pollution sources (sewage influent and effluent, industrial effluent, mine runoff) and different stages of the DW treatment process (pre-treatment, groundwater observation well, DW production well) by using the river water as raw water with an artificial groundwater recharge (AGR). The beta-diversity analysis revealed that bacterial communities were highly varied among sample groups (R = 0.92, p < 0.001, ANOSIM). The species richness and evenness indices were highest in surface water (Chao1; 920 ± 10) among sample groups and gradually decreased during the DW treatment process (DW production well; Chao1: 320 ± 20). Although the phylum Proteobacteria was omnipresent, its relative abundance was higher in sewage and industrial effluents (66–80%) than in surface water (55%). Phyla Firmicutes and Fusobacteria were only detected in sewage samples. Actinobacteria was more abundant in the surface water (≥13%) than in other groups (≤3%). Acidobacteria was more abundant in the DW treatment process (≥13%) than in others (≤2%). In total, the share of PHRB reads was higher in sewage and surface water than in the DW treatment samples. The seasonal effect in bacterial communities was observed only on surface water samples, with the lowest diversity during summer. Conclusions The low bacterial diversity and absence of PHRB read in the DW samples indicate AGR can produce biologically stable and microbiologically safe drinking water. Furthermore, the significantly different bacterial communities at the pollution sources compared to surface water and DW samples highlight the importance of effective wastewater treatment for protecting the environment and human health.

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Effect of milk replacer allowance on calf faecal bacterial community profiles and fermentation

Animal Microbiome ◽

10.1186/s42523-021-00088-2 ◽

2021 ◽

Vol 3 (1) ◽

Author(s):

Sandeep Kumar ◽

M. Ajmal Khan ◽

Emma Beijer ◽

Jinxin Liu ◽

Katherine K. Lowe ◽

...

Keyword(s):

Fatty Acids ◽

Body Weight ◽

Bacterial Community ◽

Bacterial Diversity ◽

Serum Protein ◽

Bacterial Communities ◽

Short Chain Fatty Acids ◽

Short Chain ◽

Milk Replacer ◽

Protein Levels

Abstract Background The nutrition of calves from birth until weaning is predominantly from liquid (milk or milk-based) feeds. Liquid feed allowances are often restricted during artificial rearing to accelerate the development of the rumen by promoting solid feed intake. Liquid feeds bypass the rumen and are digested in the lower digestive tract, however, the influence of different types of milk feeds, and their allowances, on the calf hindgut microbiota is not well understood. In this study, faecal samples from 199 calves raised on three different allowances of milk replacer: 10% of initial bodyweight (LA), 20% of initial bodyweight (HA), and ad libitum (ADLIB), were collected just prior to weaning. Bacterial community structures and fermentation products were analysed, and their relationships with calf growth and health parameters were examined to identify potential interactions between diet, gut microbiota and calf performance. Results Differences in the total concentrations of short-chain fatty acids were not observed, but higher milk replacer allowances increased the concentrations of branched short-chain fatty acids and decreased acetate to propionate ratios. The bacterial communities were dominated by Ruminococcaceae, Lachnospiraceae and Bacteroides, and the bacterial diversity of the ADLIB diet group was greater than that of the other diet groups. Faecalibacterium was over three times more abundant in the ADLIB compared to the LA group, and its abundance correlated strongly with girth and body weight gains. Milk replacer intake correlated strongly with Peptococcus and Blautia, which also correlated with body weight gain. Bifidobacterium averaged less than 1% abundance, however its levels, and those of Clostridium sensu stricto 1, correlated strongly with initial serum protein levels, which are an indicator of colostrum intake and passive transfer of immunoglobulins in early life. Conclusions Higher milk replacer intakes in calves increased hindgut bacterial diversity and resulted in bacterial communities and short chain fatty acid profiles associated with greater protein fermentation. Increased abundances of beneficial bacteria such as Faecalibacterium, were also observed, which may contribute to development and growth. Moreover, correlations between microbial taxa and initial serum protein levels suggest that colostrum intake in the first days of life may influence microbiota composition at pre-weaning.

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Successional trajectory of bacterial communities in soil are shaped by plant-driven changes during secondary succession

Scientific Reports ◽

10.1038/s41598-020-66638-x ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Mayank Krishna ◽

Shruti Gupta ◽

Manuel Delgado – Baquerizo ◽

Elly Morriën ◽

Satish Chandra Garkoti ◽

...

Keyword(s):

Bacterial Community ◽

Bacterial Diversity ◽

Community Composition ◽

Bacterial Communities ◽

Secondary Succession ◽

Positive Association ◽

Ecological Networks ◽

Growth Stages ◽

Ecosystem Recovery ◽

Soil Bacterial

Abstract This study investigated the potential role of a nitrogen-fixing early-coloniser Alnus Nepalensis D. Don (alder) in driving the changes in soil bacterial communities during secondary succession. We found that bacterial diversity was positively associated with alder growth during course of ecosystem development. Alder development elicited multiple changes in bacterial community composition and ecological networks. For example, the initial dominance of actinobacteria within bacterial community transitioned to the dominance of proteobacteria with stand development. Ecological networks approximating species associations tend to stabilize with alder growth. Janthinobacterium lividum, Candidatus Xiphinematobacter and Rhodoplanes were indicator species of different growth stages of alder. While the growth stages of alder has a major independent contribution to the bacterial diversity, its influence on the community composition was explained conjointly by the changes in soil properties with alder. Alder growth increased trace mineral element concentrations in the soil and explained 63% of variance in the Shannon-diversity. We also found positive association of alder with late-successional Quercus leucotrichophora (Oak). Together, the changes in soil bacterial community shaped by early-coloniser alder and its positive association with late-successional oak suggests a crucial role played by alder in ecosystem recovery of degraded habitats.

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Long-term nutrient enrichment of an oligotroph-dominated wetland increases bacterial diversity in bulk soils and plant rhizospheres

10.1101/2020.01.08.899781 ◽

2020 ◽

Author(s):

Regina B. Bledsoe ◽

Carol Goodwillie ◽

Ariane L. Peralta

Keyword(s):

Bacterial Community ◽

Bacterial Diversity ◽

Community Composition ◽

Nutrient Enrichment ◽

Bacterial Communities ◽

Nutrient Addition ◽

Soil Microbiome ◽

The Core ◽

Soil Bacterial

ABSTRACTIn nutrient-limited conditions, plants rely on rhizosphere microbial members to facilitate nutrient acquisition, and in return plants provide carbon resources to these root-associated microorganisms. However, atmospheric nutrient deposition can affect plant-microbe relationships by changing soil bacterial composition and by reducing cooperation between microbial taxa and plants. To examine how long-term nutrient addition shapes rhizosphere community composition, we compared traits associated with bacterial (fast growing copiotrophs, slow growing oligotrophs) and plant (C3 forb, C4 grass) communities residing in a nutrient poor wetland ecosystem. Results revealed that oligotrophic taxa dominated soil bacterial communities and that fertilization increased the presence of oligotrophs in bulk and rhizosphere communities. Additionally, bacterial species diversity was greatest in fertilized soils, particularly in bulk soils. Nutrient enrichment (fertilized vs. unfertilized) and plant association (bulk vs. rhizosphere) determined bacterial community composition; bacterial community structure associated with plant functional group (grass vs. forb) was similar within treatments but differed between fertilization treatments. The core forb microbiome consisted of 602 unique taxa, and the core grass microbiome consisted of 372 unique taxa. Forb rhizospheres were enriched in potentially disease suppressive bacterial taxa and grass rhizospheres were enriched in bacterial taxa associated with complex carbon decomposition. Results from this study demonstrate that fertilization serves as a strong environmental filter on the soil microbiome, which leads to distinct rhizosphere communities and can shift plant effects on the rhizosphere microbiome. These taxonomic shifts within plant rhizospheres could have implications for plant health and ecosystem functions associated with carbon and nitrogen cycling.ImportanceOver the last century, humans have substantially altered nitrogen and phosphorus cycling. Use of synthetic fertilizer and burning of fossil fuels and biomass have increased nitrogen and phosphorous deposition, which results in unintended fertilization of historically low-nutrient ecosystems. With increased nutrient availability, plant biodiversity is expected to decline and bacterial communities are anticipated to increase in abundance of copiotrophic taxa. Here, we address how bacterial communities associated with different plant functional types (forb, grass) shift due to long-term nutrient enrichment. Unlike other studies, results revealed an increase in bacterial diversity, particularly, of oligotrophic bacteria in fertilized plots. We observed that nutrient addition strongly determines forb and grass rhizosphere composition, which could indicate different metabolic preferences in the bacterial communities. This study highlights how long-term fertilization of oligotroph-dominated wetlands could alter the metabolism of rhizosphere bacterial communities in unexpected ways.

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Microbiota Dysbiosis in Fungal Rhinosinusitis

Journal of Clinical Medicine ◽

10.3390/jcm8111973 ◽

2019 ◽

Vol 8 (11) ◽

pp. 1973 ◽

Cited By ~ 3

Author(s):

Yen-Ting Lu ◽

Shao-Hung Wang ◽

Ming-Li Liou ◽

Ting-An Shen ◽

Ying-Chou Lu ◽

...

Keyword(s):

Bacterial Community ◽

16S Rrna ◽

Chronic Rhinosinusitis ◽

Bacterial Communities ◽

Middle Meatus ◽

Fungal Rhinosinusitis ◽

Bacterial Microbiota ◽

Histological Characteristics ◽

Distinct Distribution

Fungal rhinosinusitis is a unique phenotype of chronic rhinosinusitis with unique clinical and histological characteristics. The role of bacterial microbiota in various phenotypes chronic rhinosinusitis is not thoroughly understood. Therefore, we conducted 16s rRNA amplification sequencing to determine differences in bacterial communities between phenotypes (fungal vs. non- fungal) and anatomical sites (middle meatus vs. nasopharynx). Endoscope-guided swabs were used to collect samples from the middle meatus and nasopharynx of seven consecutive patients with fungal and 18 consecutive patients with non-fungal rhinosinusitis. DNA was extracted and investigated through 16S rRNA amplification. Among samples from the middle meatus, Shannon diversity was significantly lower in those from the fungal rhinosinusitis group (p = 0.029). However, no significant differences in diversity were noted between nasopharynx samples (p = 0.85). Fungal rhinosinusitis samples exhibited a distinct distribution of taxon relative abundance, which involved not only the absence of rhinosinusitis-associated commensal Corynebacterium and Fusobacterium in the middle meatus but also a significant increase in Haemophilus prevalence and abundance. This is the first study to compare bacterial communities in fungal and non-fungal rhinosinusitis samples. Our findings demonstrated that bacterial community dysbiosis was more apparent in fungal rhinosinusitis samples and was limited to the middle meatus.

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Long-Term Nutrient Enrichment of an Oligotroph-Dominated Wetland Increases Bacterial Diversity in Bulk Soils and Plant Rhizospheres

mSphere ◽

10.1128/msphere.00035-20 ◽

2020 ◽

Vol 5 (3) ◽

Author(s):

Regina B. Bledsoe ◽

Carol Goodwillie ◽

Ariane L. Peralta

Keyword(s):

Bacterial Community ◽

Bacterial Diversity ◽

Community Composition ◽

Nutrient Enrichment ◽

Bacterial Communities ◽

Nutrient Addition ◽

Nitrogen And Phosphorus ◽

The Core ◽

Soil Bacterial

ABSTRACT In nutrient-limited conditions, plants rely on rhizosphere microbial members to facilitate nutrient acquisition, and in return, plants provide carbon resources to these root-associated microorganisms. However, atmospheric nutrient deposition can affect plant-microbe relationships by changing soil bacterial composition and by reducing cooperation between microbial taxa and plants. To examine how long-term nutrient addition shapes rhizosphere community composition, we compared traits associated with bacterial (fast-growing copiotrophs, slow-growing oligotrophs) and plant (C3 forb, C4 grass) communities residing in a nutrient-poor wetland ecosystem. Results revealed that oligotrophic taxa dominated soil bacterial communities and that fertilization increased the presence of oligotrophs in bulk and rhizosphere communities. Additionally, bacterial species diversity was greatest in fertilized soils, particularly in bulk soils. Nutrient enrichment (fertilized versus unfertilized) and plant association (bulk versus rhizosphere) determined bacterial community composition; bacterial community structure associated with plant functional group (grass versus forb) was similar within treatments but differed between fertilization treatments. The core forb microbiome consisted of 602 unique taxa, and the core grass microbiome consisted of 372 unique taxa. Forb rhizospheres were enriched in potentially disease-suppressive bacterial taxa, and grass rhizospheres were enriched in bacterial taxa associated with complex carbon decomposition. Results from this study demonstrate that fertilization serves as a strong environmental filter on the soil microbiome, which leads to distinct rhizosphere communities and can shift plant effects on the rhizosphere microbiome. These taxonomic shifts within plant rhizospheres could have implications for plant health and ecosystem functions associated with carbon and nitrogen cycling. IMPORTANCE Over the last century, humans have substantially altered nitrogen and phosphorus cycling. Use of synthetic fertilizer and burning of fossil fuels and biomass have increased nitrogen and phosphorus deposition, which results in unintended fertilization of historically low-nutrient ecosystems. With increased nutrient availability, plant biodiversity is expected to decline, and the abundance of copiotrophic taxa is anticipated to increase in bacterial communities. Here, we address how bacterial communities associated with different plant functional types (forb, grass) shift due to long-term nutrient enrichment. Unlike other studies, results revealed an increase in bacterial diversity, particularly of oligotrophic bacteria in fertilized plots. We observed that nutrient addition strongly determines forb and grass rhizosphere composition, which could indicate different metabolic preferences in the bacterial communities. This study highlights how long-term fertilization of oligotroph-dominated wetlands could alter diversity and metabolism of rhizosphere bacterial communities in unexpected ways.

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Perennials but not slope aspect affect the diversity of soil bacterial communities in the northern Negev Desert, Israel

Soil Research ◽

10.1071/sr17010 ◽

2018 ◽

Vol 56 (2) ◽

pp. 123 ◽

Cited By ~ 1

Author(s):

Ahuva Vonshak ◽

Menachem Y. Sklarz ◽

Ann M. Hirsch ◽

Osnat Gillor

Keyword(s):

Bacterial Community ◽

Bacterial Diversity ◽

Community Composition ◽

Bacterial Communities ◽

Bacterial Community Composition ◽

Plant Litter ◽

Negev Desert ◽

Slope Aspect ◽

Desert Shrubs ◽

Soil Bacterial

Underneath the canopy of perennials in arid regions, moderate soil temperature and evaporation, as well as plant litter create islands of higher fertility in the low-productivity landscape, known as ‘resource islands’. The sparse distribution of these resource islands is mirrored by soil microbial communities, which mediate a large number of biogeochemical transformations underneath the plants. We explored the link between the bacterial community composition and two prevalent desert shrubs, Zygophyllum dumosum and Artemisia herba-alba, on northern- and southern-facing slopes in the northern highlands of the Negev Desert (Israel), at the end of a drought winter mild rainy season. We sequenced the bacterial community and analysed the physicochemical properties of the soil under the shrub canopies and from barren soil in replicate slopes. The soil bacterial diversity was independent of slope aspect, but differed according to shrub presence or type. Links between soil bacterial community composition and their associated desert shrubs were found, enabling us to link bacterial diversity with shrub type or barren soils. Our results suggest that plants and their associated bacterial communities are connected to survival and persistence under the harsh desert conditions.

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Soil Element Stoichiometry Drives Bacterial Community Composition Following Thinning in A Larix Plantation in the Subalpine Regions of Northern China

Forests ◽

10.3390/f11030261 ◽

2020 ◽

Vol 11 (3) ◽

pp. 261

Author(s):

Mengke Cai ◽

Xinhao Peng ◽

Xiaoqin Cheng ◽

Li Liu ◽

Shiping Xing ◽

...

Keyword(s):

Bacterial Community ◽

Community Composition ◽

High Intensity ◽

Bacterial Communities ◽

Soil Resource ◽

Low Intensity ◽

Medium Intensity ◽

Elemental Stoichiometry ◽

Tree Removal ◽

Bacterial Groups

It is well established that forest thinning alters aboveground plant community composition and soil resource availability. However, how it regulates the composition and diversity of belowground microbial communities remains unclear. To quantify the effects of thinning on soil bacterial groups and the underlying mechanisms of these effects, this research was conducted in a Larix principis-rupprechtii Mayr. plantation with various thinning intensities, including a control (0% tree removal), a low-intensity treatment (15% tree removal), a medium-intensity treatment (35% tree removal), and a high-intensity treatment (50% tree removal). Compared to the control, the medium and high intensity thinning treatments significantly improved soil moisture, nutrient concentrations (including soil total carbon, nitrogen, phosphorus, and ammonium nitrogen), microbial biomass, and elemental stoichiometry ratios. The abundance and diversity of bacterial communities peaked in the medium-intensity treatment. Thinning also had strong effects on dominant bacterial groups at the phylum level. For instance, Bacteroidetes and Nitrospirae were significantly increased in the medium-intensity treatment (MIT), while the Gemmatimonadetes were significantly decreased in the low-intensity treatment (LIT). Combining Spearman correlation analysis and redundancy analysis demonstrated that thinning could facilitate the assembly of unique bacterial communities, and these shifts in microorganisms could probably be attributed to corresponding changes in soil resource stoichiometry. In conclusion, this study provides novel evidence that rational thinning could promote belowground bacterial community diversity and that elemental stoichiometry is an important indicator in shaping forest soil bacterial communities.

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Maternal Exposure to Ozone Modulates the Endophyte-Conferred Resistance to Aphids in Lolium multiflorum Plants

Insects ◽

10.3390/insects11090548 ◽

2020 ◽

Vol 11 (9) ◽

pp. 548 ◽

Cited By ~ 1

Author(s):

Ludmila M. Bubica Bustos ◽

Andrea C. Ueno ◽

Tara D. Di Leo ◽

Carlos D. Crocco ◽

M. Alejandra Martínez-Ghersa ◽

...

Keyword(s):

Plant Biomass ◽

Lolium Multiflorum ◽

Rhopalosiphum Padi ◽

Fungal Endophytes ◽

Growth Stimulation ◽

Fungal Endophyte ◽

Stress Factors ◽

Biotic And Abiotic Stress ◽

Abiotic Stress Factors ◽

Host Growth

Plants are challenged by biotic and abiotic stress factors and the incidence of one can increase or decrease resistance to another. These relations can also occur transgenerationally. For instance, progeny plants whose mothers experienced herbivory can be more resistant to herbivores. Certain fungal endophytes that are vertically transmitted endow plants with alkaloids and resistance to herbivores. However, endophyte-symbiotic plants exposed to the oxidative agent ozone became susceptible to aphids. Here, we explored whether this effect persists transgenerationally. We exposed Lolium multiflorum plants with and without fungal endophyte Epichloë occultans to ozone (120 or 0 ppb), and then, challenged the progeny with aphids (Rhopalosiphum padi). The endophyte was the main factor determining the resistance to aphids, but its importance diminished in plants with ozone history. This negative ozone effect on the endophyte-mediated resistance was apparent on aphid individual weights. Phenolic compounds in seeds were increased by the symbiosis and diminished by the ozone. The endophyte effect on phenolics vanished in progeny plants while the negative ozone effect persisted. Independently of ozone, the symbiosis increased the plant biomass (≈24%). Although ozone can diminish the importance of endophyte symbiosis for plant resistance to herbivores, it would be compensated by host growth stimulation.

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Identifying the Biogeographic Patterns of Rare and Abundant Bacterial Communities Using Different Primer Sets on the Loess Plateau

Microorganisms ◽

10.3390/microorganisms9010139 ◽

2021 ◽

Vol 9 (1) ◽

pp. 139

Author(s):

Quanchao Zeng ◽

Shaoshan An

Keyword(s):

Community Structure ◽

Environmental Factors ◽

Bacterial Community ◽

Bacterial Diversity ◽

Bacterial Communities ◽

Land Uses ◽

The Loess Plateau ◽

Soil Bacterial Diversity ◽

Soil Bacterial ◽

Rare Bacteria

High-throughput sequencing is commonly used to study soil microbial communities. However, different primers targeting different 16S rRNA hypervariable regions often generate different microbial communities and result in different values of diversity and community structure. This study determined the consequences of using two bacterial primers (338f/806r, targeting the V3-V4 region, and 520f/802r, targeting the V4 region) to assess bacterial communities in the soils of different land uses along a latitudinal gradient. The results showed that the variations in the soil bacterial diversity in different land uses were more evident based on the former pair. The statistical results showed that land use had no significant impact on soil bacterial diversity when primer pair 520f/802r was used. In contrast, when primer pair 338f/806r was used, the cropland and orchard soils had significantly higher operational taxonomic units (OTUs) and Shannon diversity index values than those of the shrubland and grassland soils. Similarly, the soil bacterial diversity generated by primer pair 338f/806r was significantly impacted by mean annual precipitation, soil total phosphorus (TP), soil total nitrogen (TN), and soil available phosphorus (AVP), while the soil bacterial diversity generated by primer pair 520f/802r showed no significant correlations with most of these environmental factors. Multiple regression models indicated that soil pH and soil organic carbon (SOC) shaped the soil bacterial community structure on the Loess Plateau regardless of what primer pair was used. Climatic conditions mainly affected the diversity of rare bacteria. Abundant bacteria are more sensitive than rare bacteria to environmental changes. Very little of the variation in the rare bacterial community was explained by environmental factors or geographic distance, suggesting that the communities of rare bacteria are unpredictable. The distributions of the abundant taxa were mainly determined by variations in environmental factors.

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