scholarly journals Diuron tolerance and potential degradation by pelagic microbiomes in the Great Barrier Reef lagoon

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1758 ◽  
Author(s):  
Florent E. Angly ◽  
Olga Pantos ◽  
Thomas C. Morgan ◽  
Virginia Rich ◽  
Hemerson Tonin ◽  
...  
Keyword(s):  
Great Barrier Reef ◽  
Relative Abundance ◽  
Rrna Gene ◽  
Barrier Reef ◽  
Marine Food Web ◽  
Herbicide Degradation ◽  
Long Term Effect ◽  
Reef Health ◽  
Agricultural Areas ◽  
The Impact

Diuron is a herbicide commonly used in agricultural areas where excess application causes it to leach into rivers, reach sensitive marine environments like the Great Barrier Reef (GBR) lagoon and pose risks to marine life. To investigate the impact of diuron on whole prokaryotic communities that underpin the marine food web and are integral to coral reef health, GBR lagoon water was incubated with diuron at environmentally-relevant concentration (8 µg/L), and sequenced at specific time points over the following year. 16S rRNA gene amplicon profiling revealed no significant short- or long-term effect of diuron on microbiome structure. The relative abundance of prokaryotic phototrophs was not significantly altered by diuron, which suggests that they were largely tolerant at this concentration. Assembly of a metagenome derived from waters sampled at a similar location in the GBR lagoon did not reveal the presence of mutations in the cyanobacterial photosystem that could explain diuron tolerance. However, resident phages displayed several variants of this gene and could potentially play a role in tolerance acquisition. Slow biodegradation of diuron was reported in the incubation flasks, but no correlation with the relative abundance of heterotrophs was evident. Analysis of metagenomic reads supports the hypothesis that previously uncharacterized hydrolases carried by low-abundance species may mediate herbicide degradation in the GBR lagoon. Overall, this study offers evidence that pelagic phototrophs of the GBR lagoon may be more tolerant of diuron than other tropical organisms, and that heterotrophs in the microbial seed bank may have the potential to degrade diuron and alleviate local anthropogenic stresses to inshore GBR ecosystems.

Manipulation of fishing effort in Australia's penaeid Prawn Fisheries

1990 ◽  
Vol 41 (1) ◽  
pp. 1 ◽  
Author(s):  
IF Somers
Keyword(s):  
Side Effects ◽  
Great Barrier Reef ◽  
Simulation Model ◽  
Fishing Effort ◽  
Regulatory Mechanisms ◽  
Barrier Reef ◽  
Restrictive Measures ◽  
The Impact ◽  
Term Management

The potentially detrimental side-effects of prawn trawling are coming under increasing scrutiny in Australian waters, particularly in such ecologically sensitive areas as Queensland's Great Barrier Reef, and various restrictive measures are being suggested. Before changes are imposed on the prawning industry, the effects of trawling on the target prawn species and the long-term management of these effects need to be fully understood. Using a simulation model of a simplified prawn fishery, this paper describes the basis for the current regulatory mechanisms for Australian's prawn fisheries, in particular the manipulation of both the level and pattern of fishing effort. It is shown that even in moderately fished stocks, the fishery manager has several options, such as seasonal and nursery area closures, that are consistent with the goal of minimizing the impact of prawn trawling, while in no way penalizing the industry economically. With these in mind, possible ways of resolving or reducing the conflict with groups outside the prawning industry are discussed.

Economically viable land regeneration in Central Queensland and improved water quality outcomes for the Great Barrier Reef

2011 ◽  
Vol 33 (3) ◽  
pp. 267 ◽  
Author(s):  
M. Star ◽  
P. Donaghy ◽  
J. Rolfe
Keyword(s):  
Great Barrier Reef ◽  
Ground Cover ◽  
Scientific Data ◽  
Barrier Reef ◽  
Sediment Loads ◽  
Land Condition ◽  
Sediment Reduction ◽  
Grazing Lands ◽  
The Impact ◽  
Land Types

The impact of excessive sediment loads entering into the Great Barrier Reef lagoon has led to increased awareness of land condition in grazing lands. Improved ground cover and land condition have been identified as two important factors in reducing sediment loads. This paper reports the economics of land regeneration using case studies for two different land types in the Fitzroy Basin. The results suggest that for sediment reduction to be achieved from land regeneration of more fertile land types (brigalow blackbutt) the most efficient method of allocating funds would be through extension and education. However for less productive country (narrow leaved ironbark woodlands) incentives will be required. The analysis also highlights the need for further scientific data to undertake similar financial assessments of land regeneration for other locations in Queensland.

scholarly journals Assessment of the Accuracy of Recent Empirical and Assimilated Tidal Models for the Great Barrier Reef, Australia, Using Satellite and Coastal Data

2019 ◽  
Vol 11 (10) ◽  
pp. 1211 ◽  
Author(s):  
Fardin Seifi ◽  
Xiaoli Deng ◽  
Ole Baltazar Andersen
Keyword(s):  
Great Barrier Reef ◽  
Sea Level ◽  
Root Mean Square ◽  
Tide Gauge ◽  
Bottom Topography ◽  
Deep Ocean ◽  
Mean Square ◽  
Barrier Reef ◽  
In Situ Data ◽  
The Impact

The latest satellite and in situ data are a fundamental source for tidal model evaluations. In this work, the satellite missions TOPEX/Poseidon, Jason-1, Jason-2 and Sentinel-3A, together with tide gauge data, were used to investigate the performance of recent regional and global tidal models over the Great Barrier Reef, Australia. Ten models, namely, TPXO8, TPXO9, EOT11a, HAMTIDE, FES2012, FES2014, OSUNA, OSU12, GOT 4.10 and DTU10, were considered. The accuracy of eight major tidal constituents (i.e., K1, O1, P1, Q1, M2, S2, N2 and K2) and one shallow water constituent (M4) were assessed based on the analysis of sea-level observations from coastal tide gauges and altimetry data (TOPEX series). The outcome was compared for four different subregions, namely, the coastline, coastal, shelf and deep ocean zones. Sea-level anomaly data from the Sentinel-3A mission were corrected using the tidal heights predicted by each model. The root mean square values of the sea level anomalies were then compared. According to the results, FES2012 compares more favorably to other models with root mean square (RMS) values of 10.9 cm and 7.7 cm over the coastal and shelf zones, respectively. In the deeper sections, the FES2014 model compares favorably at 7.5 cm. In addition, the impact of sudden fluctuations in bottom topography on model performances suggest that a combination of bathymetric variations and proximity to the coast or islands contributes to tidal height prediction accuracies of the models.

scholarly journals Epilithic Cyanobacterial Communities of a Marine Tropical Beach Rock (Heron Island, Great Barrier Reef): Diversity and Diazotrophy

2007 ◽  
Vol 73 (11) ◽  
pp. 3656-3668 ◽  
Author(s):  
Beatriz Díez ◽  
Karolina Bauer ◽  
Birgitta Bergman
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Great Barrier Reef ◽  
Rrna Gene ◽  
Barrier Reef ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Nitrogen Fixers ◽  
Gene Optimization ◽  
Beach Rock

ABSTRACT The diversity and nitrogenase activity of epilithic marine microbes in a Holocene beach rock (Heron Island, Great Barrier Reef, Australia) with a proposed biological calcification “microbialite” origin were examined. Partial 16S rRNA gene sequences from the dominant mat (a coherent and layered pink-pigmented community spread over the beach rock) and biofilms (nonstratified, differently pigmented microbial communities of small shallow depressions) were retrieved using denaturing gradient gel electrophoresis (DGGE), and a clone library was retrieved from the dominant mat. The 16S rRNA gene sequences and morphological analyses revealed heterogeneity in the cyanobacterial distribution patterns. The nonheterocystous filamentous genus Blennothrix sp., phylogenetically related to Lyngbya, dominated the mat together with unidentified nonheterocystous filaments of members of the Pseudanabaenaceae and the unicellular genus Chroococcidiopsis. The dominance and three-dimensional intertwined distribution of these organisms were confirmed by nonintrusive scanning microscopy. In contrast, the less pronounced biofilms were dominated by the heterocystous cyanobacterial genus Calothrix, two unicellular Entophysalis morphotypes, Lyngbya spp., and members of the Pseudanabaenaceae family. Cytophaga-Flavobacterium-Bacteroides and Alphaproteobacteria phylotypes were also retrieved from the beach rock. The microbial diversity of the dominant mat was accompanied by high nocturnal nitrogenase activities (as determined by in situ acetylene reduction assays). A new DGGE nifH gene optimization approach for cyanobacterial nitrogen fixers showed that the sequences retrieved from the dominant mat were related to nonheterocystous uncultured cyanobacterial phylotypes, only distantly related to sequences of nitrogen-fixing cultured cyanobacteria. These data stress the occurrence and importance of nonheterocystous epilithic cyanobacteria, and it is hypothesized that such epilithic cyanobacteria are the principal nitrogen fixers of the Heron Island beach rock.

Analysis of the impact of prawn trawling on benthic species in the Great Barrier Reef Marine Park

2004 ◽  
Vol 15 (3) ◽  
pp. 279-289 ◽  
Author(s):  
P. J. Toscas ◽  
M. J. Faddy ◽  
C. Y. Burridge
Keyword(s):  
Great Barrier Reef ◽  
Barrier Reef ◽  
Benthic Species ◽  
Marine Park ◽  
The Impact

scholarly journals Identification and Removal of Potential Contaminants in 16S rRNA Gene Sequence Datasets from Low Microbial Biomass Samples: An Example from the Mosquito Gut

2020 ◽  
Author(s):  
Sebastián Diaz ◽  
Juan Sebastián Escobar ◽  
Frank William Avila
Keyword(s):  
Microbial Biomass ◽  
16S Rrna ◽  
Gut Microbiota ◽  
Relative Abundance ◽  
Vector Competence ◽  
Negative Control ◽  
Rrna Gene ◽  
Physiological Processes ◽  
Physiological Relevance ◽  
The Impact

Abstract Background: The bacterial gut microbiota of the female mosquito influences numerous physiological processes, including vector competence. As a low-microbial-biomass ecosystem, mosquito gut tissue is prone to contamination from the laboratory environment and from reagents commonly used to dissect and/or isolate DNA from gut tissue. In this report, we analyze five 16S rRNA datasets, including new data obtained by us, to gain insight into the impact of potential contaminating sequences on the composition, diversity, and structure of the mosquito gut microbial community. Results: We present a clustering-free approach that, based on the relative abundance of amplicon sequence variants (ASVs) in gut and negative control samples , allowed for the identification of candidate contaminating sequences. Some of these sequences belong to bacterial taxa previously identified as common contaminants in metagenomic studies; they have also been identified as part of the mosquito core gut microbiota, with putative physiological relevance for the host. By using different relative abundance cutoffs, we show that contaminating sequences have a significant impact on gut microbiota diversity and structure.Conclusions: The approach presented here allows the identification and removal of purported contaminating sequences in datasets obtained from low-microbial biomass samples. While it was exemplified with the analysis of gut microbiota from mosquitos, it can easily extend to other datasets dealing with similar technical artifacts.

scholarly journals The leaf bacterial microbiota of female and male kiwifruit plants in distinct seasons: assessing the impact of Pseudomonas syringae pv. actinidiae

2021 ◽  
Author(s):  
Aitana Ares ◽  
Joana Pereira ◽  
Eva Garcia ◽  
Joana Costa ◽  
Igor Tiago
Keyword(s):  
Bacterial Community ◽  
Pseudomonas Syringae ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Defense Mechanisms ◽  
Abiotic Factors ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Sequencing Platform ◽  
The Impact

The pandemic Pseudomonas syringae pv. actinidiae (Psa) has been compromising the production of the kiwifruit industry in major producing countries. Abiotic factors and plant gender are known to influence the disease outcome. To better understand their impact, we have determined the diversity of the leafs bacterial communities using the V5-V6 region of the 16S rRNA gene amplicon on the Illumina MiSeq sequencing platform. Healthy and diseased female and male kiwifruit plants were analyzed in two consecutive seasons: spring and autumn. This work describes whether the season, plant gender and the presence of Psa can affect the leaves bacterial community. Fifty bacterial operational taxonomic units (OTUs) were identified and assigned to five phyla distributed by 14 different families and 23 genera. The leaves of healthy female and male kiwi plants share most of the identified bacterial populations, that undergoes major seasonal changes. In both cases a substantial increase of the relative abundance of genus Methylobacterium is observed in autumn. The presence of Psa induced profound changes on leaves bacterial communities structure translated into a reduction in the relative abundance of previously dominant genera that had been found in healthy plants, namely Hymenobacter, Sphingomonas and Massilia. The impact of Psa was less pronounced in the bacterial community structure of male plants in both seasons. Some of the naturally occurring genera have the potential to act as an antagonist or as enhancers of the defense mechanisms paving the way for environmentally friendly and sustainable disease control.

scholarly journals Hill-based dissimilarity indices and null models for analysis of microbial community assembly

2020 ◽  
Author(s):  
Oskar Modin ◽  
Raquel Liébana ◽  
Soroush Sabeh-Alam ◽  
Britt-Marie Wilén ◽  
Carolina Suarez ◽  
...  
Keyword(s):  
Microbial Community ◽  
Relative Abundance ◽  
Community Assembly ◽  
Null Model ◽  
Amplicon Sequencing ◽  
Marker Genes ◽  
Rrna Gene ◽  
Data Set ◽  
Microbial Community Assembly ◽  
The Impact

Abstract Background: High-throughput amplicon sequencing of marker genes, such as the 16S rRNA gene in Bacteria and Archaea, provides a wealth of information about the composition of microbial communities. To quantify differences between samples and draw conclusions about factors affecting community assembly, dissimilarity indices are typically used. However, results are subject to several biases and data interpretation can be challenging. The Jaccard and Bray-Curtis indices, which are often used to quantify taxonomic dissimilarity, are not necessarily the most logical choices. Instead, we argue that Hill-based indices, which make it possible to systematically investigate the impact of relative abundance on dissimilarity, should be used for robust analysis of data. In combination with a null model, mechanisms of microbial community assembly can be analyzed. Here, we also introduce a new software, qdiv, which enables rapid calculations of Hill-based dissimilarity indices in combination with null models.Results: Using amplicon sequencing data from two experimental systems, aerobic granular sludge (AGS) reactors and microbial fuel cells (MFC), we show that the choices of bioinformatics pipeline and dissimilarity index can have considerable impacts on results and conclusions. Analysis of the AGS data set showed that results are sensitive to bioinformatics choices when dissimilarities between sample groups are compared with incidence-based indices. Analysis of the MFC data set with a combination of Hill-based indices and a null model revealed that random dispersal could explain the distribution of both rare and highly abundant taxa within a glucose-fed MFC whereas the distribution of taxa of intermediate relative abundance was governed by heterogeneous selection.Conclusions: Hill-based indices provides a rational framework for analysis of dissimilarity between microbial community samples. In combination with a null model, the effects of deterministic and stochastic factors on taxa of low-, intermediate-, and high relative abundance during microbial community assembly can be systematically investigated. Calculations of Hill-based dissimilarity indices in combination with a null model can be done in qdiv, which is freely available as a Python package (https://github.com/omvatten/qdiv).

scholarly journals The Impact of NOD2 Genetic Variants on the Gut Mycobiota in Crohn’s Disease Patients in Remission and in Individuals Without Gastrointestinal Inflammation

2020 ◽  
Author(s):  
Andrew Nelson ◽  
Christopher J Stewart ◽  
Nicholas A Kennedy ◽  
John K Lodge ◽  
Mark Tremelling ◽  
...  
Keyword(s):  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Relative Abundance ◽  
Mucosal Inflammation ◽  
Rrna Gene ◽  
Wild Type ◽  
Candida Spp ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
The Impact

Abstract Background and Aims Historical and emerging data implicate fungi in Crohn’s disease [CD] pathogenesis. However, a causal link between mycobiota, dysregulated immunity, and any impact of NOD2 variants remains elusive. This study aims to evaluate associations between NOD2 variants and faecal mycobiota in CD patients and non-CD subjects. Methods Faecal samples were obtained from 34 CD patients [18 NOD2 mutant, 16 NOD2 wild-type] identified from the UK IBD Genetics Consortium. To avoid confounding influence of mucosal inflammation, CD patients were in clinical remission and had a faecal calprotectin <250 μg/g; 47 non-CD subjects were included as comparator groups, including 22 matched household [four NOD2 mutant] and 25 non-household subjects with known NOD2 genotype [14 NOD2 mutant] identified by the NIHR BioResource Cambridge. Faecal mycobiota composition was determined using internal transcribed spacer 1 [ITS1] sequencing and was compared with 16S rRNA gene sequences and volatile organic compounds. Results CD was associated with higher numbers of fungal observed taxonomic units [OTUs] [p = 0.033]. Principal coordinates analysis using Jaccard index [p = 0.018] and weighted Bray-Curtis dissimilarities [p = 0.01] showed Candida spp. clustered closer to CD patients whereas Cryptococcus spp. clustered closer to non-CD. In CD, we found higher relative abundance of Ascomycota [p = 0.001] and lower relative abundance Basidiomycota [p = 0.019] phyla. An inverse relationship was found between bacterial and fungal Shannon diversity in NOD2 wild-type which was independent of CD [r = -0.349; p = 0.029]. Conclusions This study confirms compositional changes in the gut mycobiota in CD and provides evidence that fungi may play a role in CD pathogenesis. No NOD2 genotype-specific differences were observed in the faecal mycobiota.

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