scholarly journals Mega-fire in Redwood Tanoak Forest Reduces Bacterial and Fungal Richness and Selects for Pyrophilous Taxa and Traits that are Phylogenetically Conserved

2021 ◽  
Author(s):  
Dylan J. Enright ◽  
Kerri M. Frangioso ◽  
Kazuo Isobe ◽  
David M. Rizzo ◽  
Sydney I. Glassman
Keyword(s):  
Fire Suppression ◽  
Illumina Miseq ◽  
Soil Microbiome ◽  
Miseq Sequencing ◽  
Forest Types ◽  
Fire Response ◽  
Bacterial Composition ◽  
High Severity ◽  
Microbial Response ◽  
Sampling Locations

Mega-fires of unprecedented size, intensity, and socio-economic impacts have surged globally due to climate change, fire suppression, and development. Soil microbiomes are critical for post-fire plant regeneration and nutrient cycling, yet how mega-fires impact the soil microbiome remains unclear. We had a serendipitous opportunity to obtain pre- and post-fire soils from the same sampling locations because the 2016 Soberanes Fire, a mega-fire burning >500 Km2, burned with high severity throughout several of our established redwood-tanoak plots. This makes our study the first to examine microbial fire response in redwood-tanoak forests. We re-sampled soils immediately post-fire from two burned plots and one unburned plot to elucidate the effect of mega-fire on soil microbiomes. We used Illumina MiSeq sequencing of 16S and ITS1 to determine that both bacterial and fungal richness were reduced by 38-70% in burned plots, with richness unchanged in the unburned plot. Fire altered composition by 27% for bacteria and 24% for fungi, whereas the unburned plots experienced no change in fungal and negligible change in bacterial composition. We observed several pyrophilous taxa previously observed in Pinaceae forests, indicating that these microbes are likely general fire-responders across forest types. Further, the pyrophilous taxa that positively responded to fire were phylogenetically conserved, suggesting shared evolutionary traits. For bacteria, fire selected for increased Firmicutes and Actinobacteria. For fungi, fire selected for the Ascomycota classes Pezizomycetes and Eurotiomycetes and for a Basidiomycota class of heat-resistant Geminibasidiomycete yeasts. We hypothesize that microbes share analogous fire response to plants and propose a trait-based conceptual model of microbial response to fire that builds from Grimes Competitor-Stress tolerator-Ruderal framework (C-S-R) and its recent applications to microbes. Using this framework and established literature on several microbial species, we hypothesize some generalizable principals to predict which microbial taxa will respond to fire.

scholarly journals Changes in the Soil Microbiome in Eggplant Monoculture Revealed by High-Throughput Illumina MiSeq Sequencing as Influenced by Raw Garlic Stalk Amendment

2019 ◽  
Vol 20 (9) ◽  
pp. 2125 ◽  
Author(s):  
Muhammad Imran Ghani ◽  
Ahmad Ali ◽  
Muhammad Jawaad Atif ◽  
Muhammad Ali ◽  
Bakht Amin ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput ◽  
Soil Microbial Communities ◽  
Illumina Miseq ◽  
Soil Microbiome ◽  
Plant Residues ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
Community Structures ◽  
Microbial Community Structures

The incorporation of plant residues into soil can be considered a keystone sustainability factor in improving soil structure function. However, the effects of plant residue addition on the soil microbial communities involved in biochemical cycles and abiotic stress phenomena are poorly understood. In this study, experiments were conducted to evaluate the role of raw garlic stalk (RGS) amendment in avoiding monoculture-related production constraints by studying the changes in soil chemical properties and microbial community structures. RGS was applied in four different doses, namely the control (RGS0), 1% (RGS1), 3% (RGS2), and 5% (RGS3) per 100 g of soil. The RGS amendment significantly increased soil electrical conductivity (EC), N, P, K, and enzyme activity. The soil pH significantly decreased with RGS application. High-throughput Illumina MiSeq sequencing revealed significant alterations in bacterial community structures in response to RGS application. Among the 23 major taxa detected, Anaerolineaceae, Acidobacteria, and Cyanobacteria exhibited an increased abundance level. RGS2 increased some bacteria reported to be beneficial including Acidobacteria, Bacillus, and Planctomyces (by 42%, 64%, and 1% respectively). Furthermore, internal transcribed spacer (ITS) fungal regions revealed significant diversity among the different treatments, with taxa such as Chaetomium (56.2%), Acremonium (4.3%), Fusarium (4%), Aspergillus (3.4%), Sordariomycetes (3%), and Plectosphaerellaceae (2%) showing much abundance. Interestingly, Coprinellus (14%) was observed only in RGS-amended soil. RGS treatments effectively altered soil fungal community structures and reduced certain known pathogenic fungal genera, i.e., Fusarium and Acremonium. The results of the present study suggest that RGS amendment potentially affects the microbial community structures that probably affect the physiological and morphological attributes of eggplant under a plastic greenhouse vegetable cultivation system (PGVC) in monoculture.

scholarly journals Pollutant-Removing Biofilter Strains Associated with High Ammonia and Hydrogen Sulfide Removal Rate in a Livestock Wastewater Treatment Facility

2021 ◽  
Vol 13 (13) ◽  
pp. 7358
Author(s):  
Dong-Hyun Kim ◽  
Hyun-Sik Yun ◽  
Young-Saeng Kim ◽  
Jong-Guk Kim
Keyword(s):  
Wastewater Treatment ◽  
Hydrogen Sulfide ◽  
Microbial Community ◽  
Microbial Communities ◽  
Illumina Miseq ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
Treatment Facility ◽  
Livestock Wastewater ◽  
Wastewater Treatment Facility

This study analyzed the microbial community metagenomically to determine the cause of the functionality of a livestock wastewater treatment facility that can effectively remove pollutants, such as ammonia and hydrogen sulfide. Illumina MiSeq sequencing was used in analyzing the composition and structure of the microbial community, and the 16S rRNA gene was used. Through Illumina MiSeq sequencing, information such as diversity indicators as well as the composition and structure of microbial communities present in the livestock wastewater treatment facility were obtained, and differences between microbial communities present in the investigated samples were compared. The number of reads, operational taxonomic units, and species richness were lower in influent sample (NLF), where the wastewater enters, than in effluent sample (NL), in which treated wastewater is found. This difference was greater in June 2019 than in January 2020, and the removal rates of ammonia (86.93%) and hydrogen sulfide (99.72%) were also higher in June 2019. In both areas, the community composition was similar in January 2020, whereas the influent sample (NLF) and effluent sample (NL) areas in June 2019 were dominated by Proteobacteria (76.23%) and Firmicutes (67.13%), respectively. Oleiphilaceae (40.89%) and Thioalkalibacteraceae (12.91%), which are related to ammonia and hydrogen sulfide removal, respectively, were identified in influent sample (NLF) in June 2019. They were more abundant in June 2019 than in January 2020. Therefore, the functionality of the livestock wastewater treatment facility was affected by characteristics, including the composition of the microbial community. Compared to Illumina MiSeq sequencing, fewer species were isolated and identified in both areas using culture-based methods, suggesting Illumina MiSeq sequencing as a powerful tool to determine the relevance of microbial communities for pollutant removal.

Analysis of bacterial diversity of Chinese Luzhou-flavor liquor brewed in different seasons by Illumina Miseq sequencing

2016 ◽  
Vol 66 (3) ◽  
pp. 1293-1301 ◽  
Author(s):  
Weining Sun ◽  
Huazhi Xiao ◽  
Qian Peng ◽  
Qiaoge Zhang ◽  
Xingxing Li ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Illumina Miseq ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
Different Seasons

scholarly journals Comparing dental plaque microbiome diversity of extrinsic black stain in the primary dentition using Illumina MiSeq sequencing technique

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Lulu Chen ◽  
Qiong Zhang ◽  
Yan Wang ◽  
Keke Zhang ◽  
Jing Zou
Keyword(s):  
Relative Abundance ◽  
Dental Plaque ◽  
Illumina Miseq ◽  
Primary Dentition ◽  
Tooth Surface ◽  
Oral Microbiota ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
Cross Sectional ◽  
Sequencing Technique

Abstract Background Extrinsic black stain (EBS) is characterized by discrete dark dots or lines on the tooth surface. The relationship between EBS and oral microbiota in children remains elusive. The aim of this study was to compare dental plaque microbiome in EBS children with that in EBS-free children in the primary dentition. Methods The Illumina MiSeq sequencing technique was utilized in the cross-sectional pilot study to investigate the diversity and composition of the supragingival plaque microbiota from 10 EBS-positive and 10 EBS-free children. The results were analysed with nonparametric Mann-Whitney U test, Pearson Chi-Square test, Fisher’s Exact test and one-way ANOVA tests. Results We identified 13 different phyla, 22 classes, 33 orders, 54 families, 105 genera, and 227 species from a total of 52,646 high-quality sequences. Between two groups, no statistical differences were observed in the estimators of community richness and diversity at 97% similarity, as well as in the Unweighted Unifrac principal co-ordinates analysis (PCoA). At the species level, higher level of relative abundance of Actinomyces naeslundii and lower level of relative abundance of a species belonging to Candidate_division_TM7 was observed in dental plaque of EBS-positive subjects, compared to dental plaque of EBS-free subjects (P < 0.05). This indicated that some species might be involved in the EBS process. Conclusion Changes in dental plaque microbiota is possibly relevant to the process of EBS in the primary dentition.

scholarly journals MiSeq Sequencing of Salmonella enterica subsp. houtenae Isolates from a Dog Treated for Hind-Limb Paresis

2020 ◽  
Vol 9 (32) ◽  
Author(s):  
Mary L. Krath ◽  
Andrew E. Hillhouse ◽  
Sara V. Little ◽  
Sara D. Lawhon
Keyword(s):  
Cerebrospinal Fluid ◽  
Salmonella Enterica ◽  
Hind Limb ◽  
Illumina Miseq ◽  
Immunosuppressive Drugs ◽  
Clinical Isolates ◽  
Miseq Sequencing ◽  
Content Type

ABSTRACT The genomes of three clinical isolates of Salmonella enterica subsp. houtenae were sequenced using an Illumina MiSeq instrument. These isolates came from the urine and cerebrospinal fluid of a dog treated for hind-limb paresis with immunosuppressive drugs. S. enterica subsp. houtenae has also been implicated in brain infections in humans.

Developmental validation of a Nextera XT mitogenome Illumina MiSeq sequencing method for high-quality samples

2018 ◽  
Vol 34 ◽  
pp. 25-36 ◽  
Author(s):  
Michelle A. Peck ◽  
Kimberly Sturk-Andreaggi ◽  
Jacqueline T. Thomas ◽  
Robert S. Oliver ◽  
Suzanne Barritt-Ross ◽  
...  
Keyword(s):  
Illumina Miseq ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
High Quality ◽  
Sequencing Method ◽  
Developmental Validation

Older forests used by northern spotted owls functioned as fire refugia during large wildfires, 1987–2017

2021 ◽  
Author(s):  
Damon B Lesmeister ◽  
Raymond J. Davis ◽  
Stan G. Sovern ◽  
Zhiqiang Yang
Keyword(s):  
Fire Regime ◽  
Fire Severity ◽  
Weather Conditions ◽  
Fire Regimes ◽  
Bimodal Distribution ◽  
Relative Difference ◽  
Positive Trend ◽  
Forest Types ◽  
Spotted Owl ◽  
High Severity

Abstract Background The northern spotted owl (Strix occidentalis caurina) is an Endangered Species Act-listed subspecies that requires forests with old-growth characteristics for nesting. With climate change, large, severe wildfires are expected to be more common and an increasing threat to spotted owl persistence. Understanding fire severity patterns related to nesting forest can be valuable for forest management that supports conservation and recovery, especially if nesting forest functions as fire refugia (i.e., lower fire severity than surrounding landscape). We examined the relationship between fire severity and nesting forests in 472 large wildfires (> 200 ha) that occurred rangewide during 1987–2017. We mapped fire severities (unburned-low, moderate, high) within each fire using relative difference normalized burn ratios and quantified differences in severity between pre-fire nesting forest (edge and interior) and non-nesting forest. We also quantified these relationships within areas of three fire regimes (low severity, very frequent; mixed severity, frequent; high severity, infrequent). Results Averaged over all fires, the interior nesting forest burned at lower severity than edge or non-nesting forest. These relationships were consistent within the low severity, very frequent and mixed severity, frequent fire regime areas. All forest types burned at similar severity within the high severity, infrequent fire regime. During two of the most active wildfire years that also had the largest wildfires occurring in rare and extreme weather conditions, we found a bimodal distribution of fire severity in all forest types. In those years, a higher amount—and proportion—of all forest types burned at high severity. Over the duration of the study, we found a strong positive trend in the proportion of wildfires that burned at high severity in the non-nesting forests, but not in the two nesting forest types. Conclusions Under most wildfire conditions, the microclimate of interior patches of nesting forests likely mitigated fire severity and thus functioned as fire refugia. With changing climates, the future of interior forest as fire refugia is unknown, but trends suggest these older forests can dampen the effect of increased wildfire activity and thus an important component of landscape plans focused on fire resiliency.

Illumina MiSeq sequencing and network analysis the distribution and co-occurrence of bacterioplankton in Danjiangkou Reservoir, China

2020 ◽  
Vol 202 (4) ◽  
pp. 859-873 ◽  
Author(s):  
Zhao-Jin Chen ◽  
Ge Xu ◽  
Chuan-Yu Ding ◽  
Bao-Hai Zheng ◽  
Yan Chen ◽  
...  
Keyword(s):  
Network Analysis ◽  
Illumina Miseq ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
Danjiangkou Reservoir

scholarly journals Diversity of root-associated fungi of Rhododendron simsii in subtropical forests: fungal communities with high resistance to anthropogenic disturbances

2019 ◽  
Vol 30 (6) ◽  
pp. 2321-2330
Author(s):  
Yanhua Zhang ◽  
Fangping Tang ◽  
Jian Ni ◽  
Lijia Dong ◽  
Lifu Sun
Keyword(s):  
Functional Groups ◽  
Native Species ◽  
Illumina Miseq ◽  
Anthropogenic Disturbances ◽  
Temporal Variations ◽  
Fungal Communities ◽  
Secondary Forests ◽  
Forest Types ◽  
Subtropical Forests ◽  
Rhododendron Simsii

Abstract Species of the Ericaceae or heath family are widely distribute in continental ecosystems and their special ericoid mycorrhizas (ERM) are considered beneficial to their survival and persistence in variable habitats. Currently, increasing anthropogenic disturbances and improper forest management are affecting subtropical forests of China where these native species located. These activities not only affect plant communities above-ground, but also impose pressures on microbial communities below- ground. In this study, root-associated fungal communities of Rhododendron simsii in four forest types under different anthropogenic disturbances were identified using an Illumina Miseq platform, i.e., old growth forests, secondary forests with one cutting (SEC I), secondary forests with two cuttings (SEC II), and Chinese-fir plantations (PLF). Intra- and inter-annual variations were analyzed by comparing samples taken in different seasons and years. The results show that: (1) over 1000 OTUs were found in hair roots with most from the division Ascomycota and Basidiomycota belonging to different functional groups; (2) while there were a few indicator OTUs specific to different forest types, seasons and years, the proportion of shared taxa was quite large, accounting for 44.9–79.4% of the total OTUs; (3) significantly positive correlations were found between disturbance sensitivity and temporal variations in common fungal orders, and both in major fungal orders were significantly different among fungal functional groups in which putative and possible ERM fungi were highly resistant to disturbances and low temporal variations. The high disturbance resistance and temporal persistence of putative ERM fungi may be essential for the successful adaptation of R. simsii in disturbed subtropical forests of China.

Sign in / Sign up

Export Citation Format

Share Document