scholarly journals Effects of agricultural management on phyllosphere fungal diversity in vineyards and the association with adjacent native forests

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5715 ◽  
Author(s):  
Luis E. Castañeda ◽  
Toshiko Miura ◽  
Roland Sánchez ◽  
Olga Barbosa
Keyword(s):  
Community Structure ◽  
Fungal Diversity ◽  
Amplicon Sequencing ◽  
Diversity Indices ◽  
Agricultural Management ◽  
Native Forest ◽  
Natural Ecosystems ◽  
Native Forests ◽  
Unidentified Species ◽  
Sclerophyllous Forests

Agriculture is one of the main drivers of land conversion, and agriculture practices can impact on microbial diversity. Here we characterized the phyllosphere fungal diversity associated with Carménère grapevines under conventional and organic agricultural management. We also explored the fungal diversity present in the adjacent sclerophyllous forests to explore the potential role of native forest on vineyard phyllosphere. After conducting D2 and ITS2 amplicon sequencing, we found that fungal diversity indices did not change between conventional and organic vineyards, but community structure was sensitive to the agricultural management. On the other hand, we found a high proportion of shared fungal OTUs between vineyards and native forests. In addition, both habitats had similar levels of fungal diversity despite forest samples were derived from multiple plant species. In contrast, the community structure was different in both habitats. Interestingly, the native forest had more unidentified species and unique OTUs than vineyards. Forest dominant species wereAureobasidium pullulansandEndoconidioma populi, whereasDavidiella tassiana,Didymella sp., andAlternaria eichhorniaewere more abundant in vineyards. Overall, this study argues that a better understanding of the relationship native forests and agroecosystems is needed for maintaining and enhancing ecosystem services provided by natural ecosystems. Finally, knowledge of microbial communities living in the Chilean Mediterranean biome is needed for appropriate conservation management of these biomes and their classification as biodiversity hotspots.

scholarly journals Effects of agriculture management on fungal phyllosphere diversity in vineyards and its relationship with native forests

2018 ◽  
Author(s):  
Luis E Castañeda ◽  
Toshiko Miura ◽  
Roland Sánchez ◽  
Olga Barbosa
Keyword(s):  
Community Structure ◽  
Fungal Diversity ◽  
Amplicon Sequencing ◽  
Diversity Indices ◽  
Native Forest ◽  
Natural Ecosystems ◽  
Native Forests ◽  
Agriculture Management ◽  
Sclerophyllous Forests

Agriculture is one of the main drivers of land conversion and agriculture practices can impact on microbial diversity. Here we characterized the phyllosphere fungal diversity associated with Carmenere grapevines under conventional and organic agricultural management. We also explored the fungal diversity present in the adjacent sclerophyllous forests to explore the potential role of native forest on phyllosphere in vineyards. After conducting deep amplicon sequencing, no significant differences in fungal diversity indices and community structure were detected between organic and conventional vineyards, suggesting that the phyllosphere microorganisms of grapevines are highly resilient to agricultural treatments. On the other hand, we found a high proportion of shared fungal OTUs between vineyards and native forests. In addition, both habitats had similar levels of fungal diversity despite forest samples were derived from multiple plant species. In contrast, the community structure was different between habitats. Nevertheless, the native forest had more unidentified genera and OTUs unique to this habitat than did the vineyards. Cladosporium, Aureobasidium, and Endoconidioma were more abundant in vineyards, whereas Davidiella, Didymella, and Erysiphie were more abundant in forests. Overall, this study argues that a better understanding of the relationship native forests and agroecosystems is needed for maintaining and enhancing ecosystem services provided by natural ecosystems. Finally, knowledge of microbial communities living in the Chilean Mediterranean biome is needed for appropriate conservation management of these biomes and their classification as biodiversity hotspots.

scholarly journals Effects of agriculture management on fungal phyllosphere diversity in vineyards and its relationship with native forests

2018 ◽  
Author(s):  
Luis E Castañeda ◽  
Toshiko Miura ◽  
Roland Sánchez ◽  
Olga Barbosa
Keyword(s):  
Community Structure ◽  
Fungal Diversity ◽  
Amplicon Sequencing ◽  
Diversity Indices ◽  
Native Forest ◽  
Natural Ecosystems ◽  
Native Forests ◽  
Agriculture Management ◽  
Sclerophyllous Forests

Agriculture is one of the main drivers of land conversion and agriculture practices can impact on microbial diversity. Here we characterized the phyllosphere fungal diversity associated with Carmenere grapevines under conventional and organic agricultural management. We also explored the fungal diversity present in the adjacent sclerophyllous forests to explore the potential role of native forest on phyllosphere in vineyards. After conducting deep amplicon sequencing, no significant differences in fungal diversity indices and community structure were detected between organic and conventional vineyards, suggesting that the phyllosphere microorganisms of grapevines are highly resilient to agricultural treatments. On the other hand, we found a high proportion of shared fungal OTUs between vineyards and native forests. In addition, both habitats had similar levels of fungal diversity despite forest samples were derived from multiple plant species. In contrast, the community structure was different between habitats. Nevertheless, the native forest had more unidentified genera and OTUs unique to this habitat than did the vineyards. Cladosporium, Aureobasidium, and Endoconidioma were more abundant in vineyards, whereas Davidiella, Didymella, and Erysiphie were more abundant in forests. Overall, this study argues that a better understanding of the relationship native forests and agroecosystems is needed for maintaining and enhancing ecosystem services provided by natural ecosystems. Finally, knowledge of microbial communities living in the Chilean Mediterranean biome is needed for appropriate conservation management of these biomes and their classification as biodiversity hotspots.

scholarly journals Distinctive microbial communities in subzero hypersaline brines from Arctic coastal sea ice and rarely sampled cryopegs

2019 ◽  
Vol 95 (12) ◽  
Author(s):  
Zachary S Cooper ◽  
Josephine Z Rapp ◽  
Shelly D Carpenter ◽  
Go Iwahana ◽  
Hajo Eicken ◽  
...  
Keyword(s):  
Community Structure ◽  
Sea Ice ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Environmental Parameters ◽  
Amplicon Sequencing ◽  
Diversity Indices ◽  
Extracellular Polysaccharides ◽  
Rrna Gene ◽  
Alpha And Beta Diversity

ABSTRACT Hypersaline aqueous environments at subzero temperatures are known to be inhabited by microorganisms, yet information on community structure in subzero brines is very limited. Near Utqiaġvik, Alaska, we sampled subzero brines (–6°C, 115–140 ppt) from cryopegs, i.e. unfrozen sediments within permafrost that contain relic (late Pleistocene) seawater brine, as well as nearby sea-ice brines to examine microbial community composition and diversity using 16S rRNA gene amplicon sequencing. We also quantified the communities microscopically and assessed environmental parameters as possible determinants of community structure. The cryopeg brines harbored surprisingly dense bacterial communities (up to 108 cells mL–1) and millimolar levels of dissolved and particulate organic matter, extracellular polysaccharides and ammonia. Community composition and diversity differed between the two brine environments by alpha- and beta-diversity indices, with cryopeg brine communities appearing less diverse and dominated by one strain of the genus Marinobacter, also detected in other cold, hypersaline environments, including sea ice. The higher density and trend toward lower diversity in the cryopeg communities suggest that long-term stability and other features of a subzero brine are more important selective forces than in situ temperature or salinity, even when the latter are extreme.

scholarly journals Fungal diversity and community structure from coastal and barrier island beaches in the United States Gulf of Mexico

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Allison K. Walker ◽  
Brent M. Robicheau
Keyword(s):  
United States ◽  
Community Structure ◽  
Gulf Of Mexico ◽  
Oil Spill ◽  
Fungal Diversity ◽  
Diversity Indices ◽  
The United States ◽  
Fungal Communities ◽  
Morphological Data ◽  
Sand Beach

AbstractFungi are an important and understudied component of coastal biomes including sand beaches. Basic biogeographic diversity data are lacking for marine fungi in most parts of the world, despite their important role in decomposition. We examined intertidal fungal communities at several United States (US) Gulf of Mexico sand beach sites using morphology and ITS rDNA terminal restriction fragment length polymorphism (T-RFLP) analyses. Fungal biogeographical patterns from sand beach detritus (wood, emergent plant [mangrove/ saltmarsh], or marine [algae, seagrass]) from Florida, Mississippi, and Texas were investigated using diversity indices and multivariate analyses. Fungal diversity increased with decreasing latitude at our study sites. Substrate type strongly influenced fungal community structure in this region, with different fungal communities on detrital marine versus emergent substrates, as well as detrital marine versus wood substrates. Thirty-five fungi were identified morphologically, including new regional and host records. Of these, 86% were unique to an individual collection (i.e., sampled once from one site). Rarefaction curves from pooled morphological data from all sites estimate the number of samples required to characterize the mycota of each substrate. As sampling occurred before the Deepwater Horizon oil spill (April-2010), our findings contribute pre-oil spill sand beach biodiversity data and marine fungal distribution trends within this economically important oceanographic region.

scholarly journals Multiple bacteria associated with the more dysbiotic genitourinary microbiomes in patients with type 2 diabetes mellitus

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hua Zha ◽  
Fengping Liu ◽  
Zongxin Ling ◽  
Kevin Chang ◽  
Jiezuan Yang ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Type 2 Diabetes ◽  
Type 2 Diabetes Mellitus ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Diversity Indices ◽  
Vital Role ◽  
Rrna Gene ◽  
Beta Glucosidase

AbstractType 2 diabetes mellitus (T2DM) influences the human health and can cause significant illnesses. The genitourinary microbiome profiles in the T2DM patients remain poorly understood. In the current study, a series of bioinformatic and statistical analyses were carried out to determine the multiple bacteria associated with the more dysbiotic genitourinary microbiomes (i.e., those with lower dysbiosis ratio) in T2DM patients, which were sequenced by Illumina-based 16S rRNA gene amplicon sequencing. All the genitourinary microbiomes from 70 patients with T2DM were clustered into three clusters of microbiome profiles, i.e., Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, with Cluster_3_T2DM at the most dysbiotic genitourinary microbial status. The three clustered T2DM microbiomes were determined with different levels of alpha diversity indices, and driven by distinct urinalysis variables. OTU12_Clostridiales and OTU28_Oscillospira were likely to drive the T2DM microbiomes to more dysbiotic status, while OTU34_Finegoldia could play a vital role in maintaining the least dysbiotic T2DM microbiome (i.e., Cluster_1_T2DM). The functional metabolites K08300_ribonuclease E, K01223_6-phospho-beta-glucosidase and K00029_malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) were most associated with Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, respectively. The characteristics and multiple bacteria associated with the more dysbiotic genitourinary microbiomes in T2DM patients may help with the better diagnosis and management of genitourinary dysbiosis in T2DM patients.

Microbial community structure and trichloroethylene degradation in groundwater

2005 ◽  
Vol 51 (6) ◽  
pp. 433-439 ◽  
Author(s):  
J A Humphries ◽  
A M.H Ashe ◽  
J A Smiley ◽  
C G Johnston
Keyword(s):  
Community Structure ◽  
Clone Library ◽  
Sequence Data ◽  
Restriction Analysis ◽  
Diversity Indices ◽  
Department Of Energy ◽  
Tetrazolium Chloride ◽  
Degrading Bacteria ◽  
Trichloroethylene Degradation ◽  
Rdna Clone

Trichloroethylene (TCE) is a prevalent contaminant of groundwater that can be cometabolically degraded by indigenous microbes. Groundwater contaminated with TCE from a US Department of Energy site in Ohio was used to characterize the site-specific impact of phenol on the indigenous bacterial community for use as a possible remedial strategy. Incubations of14C-TCE-spiked groundwater amended with phenol showed increased TCE mineralization compared with unamended groundwater. Community structure was determined using DNA directly extracted from groundwater samples. This DNA was then analyzed by amplified ribosomal DNA restriction analysis. Unique restriction fragment length polymorphisms defined operational taxonomic units that were sequenced to determine phylogeny. DNA sequence data indicated that known TCE-degrading bacteria including relatives of Variovorax and Burkholderia were present in site water. Diversity of the amplified microbial rDNA clone library was lower in phenol-amended communities than in unamended groundwater (i.e., having Shannon–Weaver diversity indices of 2.0 and 2.2, respectively). Microbial activity was higher in phenol-amended ground water as determined by measuring the reduction of 2-(p-iodophenyl)-3(p-nitrophenyl)-5-phenyl tetrazolium chloride. Thus phenol amendments to groundwater correlated with increased TCE mineralization, a decrease in diversity of the amplified microbial rDNA clone library, and increased microbial activity.Key words: community structure, trichloroethylene, degradation, groundwater.

scholarly journals The use of diversity indices for local assessment of marine sediment quality

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shinya Hosokawa ◽  
Kyosuke Momota ◽  
Anthony A. Chariton ◽  
Ryoji Naito ◽  
Yoshiyuki Nakamura
Keyword(s):  
Community Structure ◽  
Sample Size ◽  
Small Sample Size ◽  
Benthic Communities ◽  
Sediment Quality ◽  
Diversity Indices ◽  
Small Sample ◽  
Species Density ◽  
Local Case ◽  
Two Indices

AbstractDiversity indices are commonly used to measure changes in marine benthic communities. However, the reliability (and therefore suitability) of these indices for detecting environmental change is often unclear because of small sample size and the inappropriate choice of communities for analysis. This study explored uncertainties in taxonomic density and two indices of community structure in our target region, Japan, and in two local areas within this region, and explored potential solutions. Our analysis of the Japanese regional dataset showed a decrease in family density and a dominance of a few species as sediment conditions become degraded. Local case studies showed that species density is affected by sediment degradation at sites where multiple communities coexist. However, two indices of community structure could become insensitive because of masking by community variability, and small sample size sometimes caused misleading or inaccurate estimates of these indices. We conclude that species density is a sensitive indicator of change in marine benthic communities, and emphasise that indices of community structure should only be used when the community structure of the target community is distinguishable from other coexisting communities and there is sufficient sample size.

scholarly journals Archaeal ammonia oxidizers respond to soil factors at smaller spatial scales than the overall archaeal community does in a high Arctic polar oasis

2016 ◽  
Vol 62 (6) ◽  
pp. 485-491 ◽  
Author(s):  
Samiran Banerjee ◽  
Nabla Kennedy ◽  
Alan E. Richardson ◽  
Keith N. Egger ◽  
Steven D. Siciliano
Keyword(s):  
Community Structure ◽  
Spatial Scales ◽  
Archaeal Community ◽  
Diversity Indices ◽  
High Arctic ◽  
Total Carbon ◽  
Spatial Dependency ◽  
Edaphic Factors ◽  
Total Carbon Content ◽  
Arctic Soils

Archaea are ubiquitous and highly abundant in Arctic soils. Because of their oligotrophic nature, archaea play an important role in biogeochemical processes in nutrient-limited Arctic soils. With the existing knowledge of high archaeal abundance and functional potential in Arctic soils, this study employed terminal restriction fragment length polymorphism (t-RFLP) profiling and geostatistical analysis to explore spatial dependency and edaphic determinants of the overall archaeal (ARC) and ammonia-oxidizing archaeal (AOA) communities in a high Arctic polar oasis soil. ARC communities were spatially dependent at the 2–5 m scale (P < 0.05), whereas AOA communities were dependent at the ∼1 m scale (P < 0.0001). Soil moisture, pH, and total carbon content were key edaphic factors driving both the ARC and AOA community structure. However, AOA evenness had simultaneous correlations with dissolved organic nitrogen and mineral nitrogen, indicating a possible niche differentiation for AOA in which dry mineral and wet organic soil microsites support different AOA genotypes. Richness, evenness, and diversity indices of both ARC and AOA communities showed high spatial dependency along the landscape and resembled scaling of edaphic factors. The spatial link between archaeal community structure and soil resources found in this study has implications for predictive understanding of archaea-driven processes in polar oases.

Impacts of switching tillage to no-tillage and vice versa on soil structure, enzyme activities, and prokaryotic community profiles in Argentinean semi-arid soils

2021 ◽  
Author(s):  
L A Gabbarini ◽  
E Figuerola ◽  
J P Frene ◽  
N B Robledo ◽  
F M Ibarbalz ◽  
...  
Keyword(s):  
Community Structure ◽  
Soil Structure ◽  
Management Practices ◽  
Soil Health ◽  
Amplicon Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Prokaryotic Community ◽  
C Cycle

Abstract The effects of tillage on soil structure, physiology, and microbiota structure were studied in a long-term field experiment, with side-to-side plots, established to compare effects of conventional tillage (CT) vs. no-till (NT) agriculture. After 27 years, part of the field under CT was switched to NT and vice versa. Soil texture, soil enzymatic profiles, and the prokaryotic community structure (16S rRNA genes amplicon sequencing) were analysed at two soil depths (0–5, 5–10 cm) in samples taken 6, 18, and 30 months after switching tillage practices. Soil enzymatic activities were higher in NT than CT, and enzymatic profiles responded to the changes much earlier than the overall prokaryotic community structure. Beta diversity measurements of the prokaryotic community indicated that the levels of stratification observed in long-term NT soils were already recovered in the new NT soils thirty months after switching from CT to NT. Bacteria and Archaea OTUs, which responded to NT were associated with coarse soil fraction, SOC and C cycle enzymes while CT responders were related to fine soil fractions and S cycle enzymes. This study showed the potential of managing the soil prokaryotic community and soil health through changes in agricultural management practices.

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