Insights into Endophytic Bacterial Diversity of Rice Grown Across the Different Agro-ecological Regions of West Bengal, India

Abstract Endophytes have recently garnered importance worldwide and multiple studies are being conducted to understand their important role and mechanism of interaction inside plants. But before we indulge in their functions it is necessary to dig into the microbiome. This will help to get a complete picture of the microbes intrinsic to their host and understand changes in community composition with respect to their habitats. To fulfil this requirement in our study we have attempted to dissect the endophytic diversity in roots of rice plant grown across the various agro-ecological zones of West Bengal by undergoing amplicon analysis of their 16S rRNA gene. We found that the agro-ecological zones can be divided into two groups: nutrient dense (GAZ, NHZ and TTAZ) and nutrient low groups (CSZ, RLZ and VAZ). Few genera (Aeromonas, Sulfurospirillum, Uliginosibacterium, etc.) are present in samples cultivated in all the zones representing the core microbiome of rice in West Bengal while some other genera like Lactococcus, Dickeya, Azonexus, Pectobacterium, etc. are unique to specific zone. It can be concluded that understanding which particular endophytes cohabit with the internal plant environment can play an important role in endophyte-based stress management strategy.

Download Full-text

Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago, Antarctica

Marine Drugs ◽

10.3390/md18060298 ◽

2020 ◽

Vol 18 (6) ◽

pp. 298

Author(s):

Alison E. Murray ◽

Nicole E. Avalon ◽

Lucas Bishop ◽

Karen W. Davenport ◽

Erwan Delage ◽

...

Keyword(s):

Marine Invertebrate ◽

Bioactive Compound ◽

Rrna Gene ◽

Sequence Variants ◽

Specific Sequence ◽

Core Microbiome ◽

Microbiome Composition ◽

The Core ◽

Synoicum Adareanum ◽

Palmerolide A

Polar marine ecosystems hold the potential for bioactive compound biodiscovery, based on their untapped macro- and microorganism diversity. Characterization of polar benthic marine invertebrate-associated microbiomes is limited to few studies. This study was motivated by our interest in better understanding the microbiome structure and composition of the ascidian, Synoicum adareanum, in which palmerolide A (PalA), a bioactive macrolide with specificity against melanoma, was isolated. PalA bears structural resemblance to a hybrid nonribosomal peptide-polyketide that has similarities to microbially-produced macrolides. We conducted a spatial survey to assess both PalA levels and microbiome composition in S. adareanum in a region of the Antarctic Peninsula near Anvers Island (64°46′ S, 64°03′ W). PalA was ubiquitous and abundant across a collection of 21 ascidians (3 subsamples each) sampled from seven sites across the Anvers Island Archipelago. The microbiome composition (V3–V4 16S rRNA gene sequence variants) of these 63 samples revealed a core suite of 21 bacterial amplicon sequence variants (ASVs)—20 of which were distinct from regional bacterioplankton. ASV co-occurrence analysis across all 63 samples yielded subgroups of taxa that may be interacting biologically (interacting subsystems) and, although the levels of PalA detected were not found to correlate with specific sequence variants, the core members appeared to occur in a preferred optimum and tolerance range of PalA levels. These results, together with an analysis of the biosynthetic potential of related microbiome taxa, describe a conserved, high-latitude core microbiome with unique composition and substantial promise for natural product biosynthesis that likely influences the ecology of the holobiont.

Download Full-text

The bacteriome of the oral cavity in healthy dogs and dogs with periodontal disease

American Journal of Veterinary Research ◽

10.2460/ajvr.21.02.0027 ◽

2022 ◽

pp. 1-9

Author(s):

Brook A. Niemiec ◽

Jerzy Gawor ◽

Shuiquan Tang ◽

Aishani Prem ◽

Janina A. Krumbeck

Keyword(s):

Oral Cavity ◽

Periodontal Disease ◽

Bacterial Species ◽

Abundant Species ◽

Rrna Gene ◽

Core Microbiome ◽

The Core ◽

Severe Periodontal Disease ◽

Healthy Dogs ◽

V3 Region

Abstract OBJECTIVE To compare the bacteriome of the oral cavity in healthy dogs and dogs with various stages of periodontal disease. ANIMALS Dogs without periodontal disease (n = 12) or with mild (10), moderate (19), or severe (10) periodontal disease. PROCEDURES The maxillary arcade of each dog was sampled with a sterile swab, and swabs were submitted for next-generation DNA sequencing targeting the V1–V3 region of the 16S rRNA gene. RESULTS 714 bacterial species from 177 families were identified. The 3 most frequently found bacterial species were Actinomyces sp (48/51 samples), Porphyromonas cangingivalis (47/51 samples), and a Campylobacter sp (48/51 samples). The most abundant species were P cangingivalis, Porphyromonas gulae, and an undefined Porphyromonas sp. Porphyromonas cangingivalis and Campylobacter sp were part of the core microbiome shared among the 4 groups, and P gulae, which was significantly enriched in dogs with severe periodontal disease, was part of the core microbiome shared between all groups except dogs without periodontal disease. Christensenellaceae sp, Bacteroidales sp, Family XIII sp, Methanobrevibacter oralis, Peptostreptococcus canis, and Tannerella sp formed a unique core microbiome in dogs with severe periodontal disease. CONCLUSIONS AND CLINICAL RELEVANCE Results highlighted that in dogs, potential pathogens can be common members of the oral cavity bacteriome in the absence of disease, and changes in the relative abundance of certain members of the bacteriome can be associated with severity of periodontal disease. Future studies may aim to determine whether these changes are the cause or result of periodontal disease or the host immune response.

Download Full-text

The Oral Microbiome of Healthy Japanese People at the Age of 90

Applied Sciences ◽

10.3390/app10186450 ◽

2020 ◽

Vol 10 (18) ◽

pp. 6450 ◽

Cited By ~ 2

Author(s):

Yoshiaki Nomura ◽

Erika Kakuta ◽

Noboru Kaneko ◽

Kaname Nohno ◽

Akihiro Yoshihara ◽

...

Keyword(s):

Human Microbiome ◽

Oral Microbiome ◽

Rrna Gene ◽

Core Microbiome ◽

Operational Taxonomic Units ◽

The Core ◽

Hypervariable Regions ◽

Study Population ◽

Granulicatella Adiacens

For a healthy oral cavity, maintaining a healthy microbiome is essential. However, data on healthy microbiomes are not sufficient. To determine the nature of the core microbiome, the oral-microbiome structure was analyzed using pyrosequencing data. Saliva samples were obtained from healthy 90-year-old participants who attended the 20-year follow-up Niigata cohort study. A total of 85 people participated in the health checkups. The study population consisted of 40 male and 45 female participants. Stimulated saliva samples were obtained by chewing paraffin wax for 5 min. The V3–V4 hypervariable regions of the 16S ribosomal RNA (rRNA) gene were amplified by PCR. Pyrosequencing was performed using MiSeq. Operational taxonomic units (OTUs) were assigned on the basis of a 97% identity search in the EzTaxon-e database. Using the threshold of 100% detection on the species level, 13 species were detected: Streptococcus sinensis, Streptococcus pneumoniae, Streptococcus salivarius, KV831974_s, Streptococcus parasanguinis, Veillonella dispar, Granulicatella adiacens, Streptococcus_uc, Streptococcus peroris, KE952139_s, Veillonella parvula, Atopobium parvulum, and AFQU_vs. These species represent potential candidates for the core make-up of the human microbiome.

Download Full-text

Analysis of Hindgut Microbiome of Sheep and Effect of Different Husbandry Conditions

Animals ◽

10.3390/ani11010004 ◽

2020 ◽

Vol 11 (1) ◽

pp. 4

Author(s):

Giulietta Minozzi ◽

Filippo Biscarini ◽

Emanuela Dalla Costa ◽

Matteo Chincarini ◽

Nicola Ferri ◽

...

Keyword(s):

Animal Health ◽

Control Group ◽

P Value ◽

Rrna Gene ◽

Microbial Composition ◽

Core Microbiome ◽

Fecal Microbiome ◽

Microbiome Composition ◽

The Core ◽

Wide Range

The microbiome is now seen as an important resource to understand animal health and welfare in many species. However, there are few studies aiming at identifying the association between fecal microbiome composition and husbandry conditions in sheep. A wide range of stressors associated with management and housing of animals increases the hypothalamic–pituitary axis activity, with growing evidence that the microbiome composition can be modified. Therefore, the purpose of the present study was to describe the core microbiome in sheep, characterized using 16S rRNA gene sequencing, and to explore whether exposure to stressful husbandry conditions changed sheep hindgut microbiome composition. Sheep (n = 10) were divided in two groups: isolated group (individually separated for 3 h/day) and control group (housed in the home pen for the entire trial period). Sheep core microbiome was dominated by Firmicutes (43.6%), Bacteroidetes (30.38%), Proteobacteria (10.14%), and Verrucomicrobia (7.55%). Comparative results revealed few operational taxonomic units (OTUs) with significantly different relative abundance between groups. Chao1, abundance-based coverage estimator (ACE), and Fisher’s alpha indices did not show differences between groups. OTU-based Bray–Curtis distances between groups were not significant (p-value = 0.07). In conclusion, these results describing the core microbiome of sheep do not suggest a strong effect of stressful husbandry conditions on microbial composition.

Download Full-text

Plant Health and Sound Vibration: Analyzing Implications of the Microbiome in Grape Wine Leaves

Pathogens ◽

10.3390/pathogens10010063 ◽

2021 ◽

Vol 10 (1) ◽

pp. 63

Author(s):

Birgit Wassermann ◽

Lise Korsten ◽

Gabriele Berg

Keyword(s):

Plant Pathogens ◽

Classical Music ◽

Antagonistic Effect ◽

Plant Health ◽

Control Group ◽

Rrna Gene ◽

Native Plant ◽

Core Microbiome ◽

The Core ◽

Sound Vibration

Understanding the plant microbiome is a key for plant health and controlling pathogens. Recent studies have shown that plants are responsive towards natural and synthetic sound vibration (SV) by perception and signal transduction, which resulted in resistance towards plant pathogens. However, whether or not native plant microbiomes respond to SV and the underlying mechanism thereof remains unknown. Within the present study we compared grapevine-associated microbiota that was perpetually exposed to classical music with a non-exposed control group from the same vineyard in Stellenbosch, South Africa. By analyzing the 16S rRNA gene and ITS fragment amplicon libraries we found differences between the core microbiome of SV-exposed leaves and the control group. For several of these different genera, e.g., Bacillus, Kocuria and Sphingomonas, a host-beneficial or pathogen-antagonistic effect has been well studied. Moreover, abundances of taxa identified as potential producers of volatile organic compounds that contribute to sensory characteristics of wines, e.g., Methylobacterium, Sphingomonas, Bacillus and Sporobolomyces roseus, were either increased or even unique within the core music-exposed phyllosphere population. Results show an as yet unexplored avenue for improved plant health and the terroir of wine, which are important for environmentally friendly horticulture and consumer appreciation. Although our findings explain one detail of the long-term positive experience to improve grapevine’s resilience by this unusual but innovative technique, more mechanistic studies are necessary to understand the whole interplay.

Download Full-text

Uncovering the core microbiome and distributions of palmerolide in Synoicum adareanum across the Anvers Island archipelago, Antarctica

10.1101/2020.02.20.958975 ◽

2020 ◽

Author(s):

Alison Murray ◽

Nicole Avalon ◽

Lucas Bishop ◽

Karen W. Davenport ◽

Erwan Delage ◽

...

Keyword(s):

Specific Activity ◽

Marine Invertebrate ◽

Bioactive Compound ◽

Rrna Gene ◽

Sequence Variants ◽

Specific Sequence ◽

Core Microbiome ◽

Microbiome Composition ◽

The Core ◽

Synoicum Adareanum

AbstractPolar marine ecosystems hold the potential for bioactive compound biodiscovery, based on their untapped macro- and microorganismal diversity. Characterization of polar benthic marine invertebrate-associated microbiomes is limited to few studies. This study was motivated by our interest in better understanding the microbiome structure and composition of the ascidian, Synoicum adareanum, in which the bioactive macrolide that has specific activity to melanoma, palmerolide A (PalA), was found. PalA bears structural resemblance to a combined nonribosomal peptide polyketide, that has similarities to microbially-produced macrolides. We conducted a spatial survey to assess both PalA levels and microbiome composition in S. adareanum in a region of the Antarctic Peninsula near Anvers Island (64° 46'S, 64° 03'W). PalA was ubiquitous and abundant across a collection of 21 ascidians (3 subsamples each) sampled from seven sites across the Anvers Island archipelago. The microbiome composition (V3-V4 16S rRNA gene sequence variants) of these 63 samples revealed a core suite of 21 bacteria, 20 of which were distinct from regional bacterioplankton. Co-occurrence analysis yielded several potentially interacting subsystems and, although the levels of PalA detected were not found to correlate with specific sequence variants, the core members appeared to occur in a preferred optimum and tolerance range of PalA levels. Taking these results together with an analysis of biosynthetic potential of related microbiome taxa indicates a core microbiome with substantial promise for natural product biosynthesis that likely interact with the host and with each other.

Download Full-text

Morphological variability inRhizoctonia solaniisolates from different agro-ecological zones of West Bengal, India

Archives of Phytopathology and Plant Protection ◽

10.1080/03235408.2013.820388 ◽

2013 ◽

Vol 47 (6) ◽

pp. 728-736 ◽

Cited By ~ 3

Author(s):

S.P. Kuiry ◽

A. Mondal ◽

S. Banerjee ◽

S. Dutta

Keyword(s):

West Bengal ◽

Morphological Variability ◽

Ecological Zones ◽

Agro Ecological Zones

Download Full-text

Differential Adaptation Strategies By Agro-Ecological Zones In African Livestock Management

10.1596/1813-9450-4601 ◽

2008 ◽

Cited By ~ 3

Author(s):

S. Niggol Seo ◽

Robert Mendelsohn ◽

Ariel Dinar ◽

Pradeep Kurukulasuriya

Keyword(s):

Adaptation Strategies ◽

Ecological Zones ◽

Livestock Management ◽

Differential Adaptation ◽

Agro Ecological Zones

Download Full-text

Towards Understanding Variability in Droughts in Response to Extreme Climate Conditions over the Different Agro-Ecological Zones of Pakistan

Sustainability ◽

10.3390/su13126910 ◽

2021 ◽

Vol 13 (12) ◽

pp. 6910

Author(s):

Adil Dilawar ◽

Baozhang Chen ◽

Arfan Arshad ◽

Lifeng Guo ◽

Muhammad Irfan Ehsan ◽

...

Keyword(s):

Pearson Correlation ◽

Principal Component ◽

Mitigation Strategies ◽

Precipitation Extremes ◽

Climate Mitigation ◽

Mean Annual Temperature ◽

Climate Extreme ◽

Ecological Zones ◽

The Mean ◽

Agro Ecological Zones

Here, we provided a comprehensive analysis of long-term drought and climate extreme patterns in the agro ecological zones (AEZs) of Pakistan during 1980–2019. Drought trends were investigated using the standardized precipitation evapotranspiration index (SPEI) at various timescales (SPEI-1, SPEI-3, SPEI-6, and SPEI-12). The results showed that droughts (seasonal and annual) were more persistent and severe in the southern, southwestern, southeastern, and central parts of the region. Drought exacerbated with slopes of −0.02, −0.07, −0.08, −0.01, and −0.02 per year. Drought prevailed in all AEZs in the spring season. The majority of AEZs in Pakistan’s southern, middle, and southwestern regions had experienced substantial warming. The mean annual temperature minimum (Tmin) increased faster than the mean annual temperature maximum (Tmax) in all zones. Precipitation decreased in the southern, northern, central, and southwestern parts of the region. Principal component analysis (PCA) revealed a robust increase in temperature extremes with a variance of 76% and a decrease in precipitation extremes with a variance of 91% in the region. Temperature and precipitation extremes indices had a strong Pearson correlation with drought events. Higher temperatures resulted in extreme drought (dry conditions), while higher precipitation levels resulted in wetting conditions (no drought) in different AEZs. In most AEZs, drought occurrences were more responsive to precipitation. The current findings are helpful for climate mitigation strategies and specific zonal efforts are needed to alleviate the environmental and societal impacts of drought.

Download Full-text