scholarly journals Island biogeography on a micro-scale: Larger anammox granules not only harbor higher species diversity but also support more functional diversity

2020 ◽  
Author(s):  
Hui Chen ◽  
Tao Liu ◽  
Jie Li ◽  
Likai Mao ◽  
Jun Ye ◽  
...  
Keyword(s):  
Species Diversity ◽  
Functional Diversity ◽  
Island Biogeography ◽  
Ecological Model ◽  
De Novo ◽  
Strong Relationship ◽  
Anammox Bacteria ◽  
Rrna Gene ◽  
Micro Scale ◽  
Theory Of Island Biogeography

Abstract Background: According to the theory of island biogeography, there is a strong relationship between the species diversity and the isolated area. However, it is unclear whether the ecological distribution of microorganisms follows this island biogeography pattern at micro-scale. Here, we use microbial granules harvested from a partial nitritation and anammox (PN/A) system as a model to test if the microbial and functional diversity follow the island biogeography. We collected and divided these granules into five discrete size-fractions (<0.2, 0.2–0.5, 0.5–0.8, 0.8–1.0 and >1.0 mm).Results: By comparing the composition and functional attribute of five pools of the size-fractionated granules by 16S rRNA gene amplicon, metagenomic and metatranscriptomic sequencing, larger granules were shown not only to harbor higher microbial diversity, but also to support more diverse functions than smaller granules. De novo co-assembly and binning of metagenomic reads yielded 22 near-complete genomes of dominant microorganisms, which allowed us to infer an ecological model of the microbial ecosystem in anammox-based granules. This genome-based ecological model indicates that nitrifying organisms in smaller granules feed nitrite to anammox bacteria in larger granules.Conclusion: Our findings substantiate that microbial communities in PN/A granules follow a species-volume relationship, suggesting the generality of the theory of island biogeography on microscopic scale.

The theory of island biogeography and soundscapes: Species diversity and the organization of acoustic communities

2019 ◽  
Vol 46 (9) ◽  
pp. 1901-1911
Author(s):  
Aloïs Robert ◽  
Thierry Lengagne ◽  
Martim Melo ◽  
Vanessa Gardette ◽  
Sacha Julien ◽  
...  
Keyword(s):  
Species Diversity ◽  
Island Biogeography ◽  
Theory Of Island Biogeography

scholarly journals A Differential Metabarcoding Approach to Describe Taxonomy Profiles of Bacteria and Archaea in the Saltern of Margherita di Savoia (Italy)

2020 ◽  
Vol 8 (6) ◽  
pp. 936 ◽  
Author(s):  
Claudia Leoni ◽  
Mariateresa Volpicella ◽  
Bruno Fosso ◽  
Caterina Manzari ◽  
Elisabetta Piancone ◽  
...  
Keyword(s):  
Ecological Model ◽  
Salinity Range ◽  
Rrna Gene ◽  
Hypervariable Regions ◽  
Cell Counts ◽  
Precious Resource ◽  
Catalyzed Reporter Deposition ◽  
Card Fish ◽  
The 16S Rrna Gene

Microorganisms inhabiting saline environments are an interesting ecological model for the study of the adaptation of organisms to extreme living conditions and constitute a precious resource of enzymes and bioproducts for biotechnological applications. We analyzed the microbial communities in nine ponds with increasing salt concentrations (salinity range 4.9–36.0%) of the Saltern of Margherita di Savoia (Italy), the largest thalassohaline saltern in Europe. A deep-metabarcoding NGS procedure addressing separately the V5-V6 and V3-V4 hypervariable regions of the 16S rRNA gene of Bacteria and Archaea, respectively, and a CARD-FISH (catalyzed reporter deposition fluorescence in situ hybridization) analysis allowed us to profile the dynamics of microbial populations at the different salt concentrations. Both the domains were detected throughout the saltern, even if the low relative abundance of Archaea in the three ponds with the lowest salinities prevented the construction of the relative amplicon libraries. The highest cell counts were recorded at 14.5% salinity for Bacteria and at 24.1% salinity for Archaea. While Bacteria showed the greatest number of genera in the first ponds (salinity range 4.9–14.5%), archaeal genera were more numerous in the last ponds of the saltern (salinity 24.1–36.0%). Among prokaryotes, Salinibacter was the genus with the maximum abundance (~49% at 34.6% salinity). Other genera detected at high abundance were the archaeal Haloquadratum (~43% at 36.0% salinity) and Natronomonas (~18% at 13.1% salinity) and the bacterial “Candidatus Aquiluna” (~19% at 14.5% salinity). Interestingly, “Candidatus Aquiluna” had not been identified before in thalassohaline waters.

scholarly journals Development of downflow hanging sponge (DHS) reactor as post treatment of existing combined anaerobic tank treating natural rubber processing wastewater

2016 ◽  
Vol 75 (1) ◽  
pp. 57-68 ◽  
Author(s):  
Takahiro Watari ◽  
Trung Cuong Mai ◽  
Daisuke Tanikawa ◽  
Yuga Hirakata ◽  
Masashi Hatamoto ◽  
...  
Keyword(s):  
Natural Rubber ◽  
Loading Rate ◽  
Oxygen Demand ◽  
Nitrogen Loading ◽  
Post Treatment ◽  
Organic Loading Rate ◽  
Anammox Bacteria ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Reactor Performance

Conventional aerated tank technology is widely applied for post treatment of natural rubber processing wastewater in Southeast Asia; however, a long hydraulic retention time (HRT) is required and the effluent standards are exceeded. In this study, a downflow hanging sponge (DHS) reactor was installed as post treatment of anaerobic tank effluent in a natural rubber factory in South Vietnam and the process performance was evaluated. The DHS reactor demonstrated removal efficiencies of 64.2 ± 7.5% and 55.3 ± 19.2% for total chemical oxygen demand (COD) and total nitrogen, respectively, with an organic loading rate of 0.97 ± 0.03 kg-COD m−3 day−1 and a nitrogen loading rate of 0.57 ± 0.21 kg-N m−3 day−1. 16S rRNA gene sequencing analysis of the sludge retained in the DHS also corresponded to the result of reactor performance, and both nitrifying and denitrifying bacteria were detected in the sponge carrier. In addition, anammox bacteria was found in the retained sludge. The DHS reactor reduced the HRT of 30 days to 4.8 h compared with the existing algal tank. This result indicates that the DHS reactor could be an appropriate post treatment for the existing anaerobic tank for natural rubber processing wastewater treatment.

The relationship between species diversity and functional diversity along aridity gradients in semi-arid rangeland

2021 ◽  
Vol 195 ◽  
pp. 104632
Author(s):  
Guy Dovrat ◽  
Ehud Meron ◽  
Moshe Shachak ◽  
Yosef Moshe ◽  
Yagil Osem
Keyword(s):  
Species Diversity ◽  
Functional Diversity ◽  
The Relationship ◽  
Semi Arid ◽  
Arid Rangeland

A natural case of RIP: degeneration of the DNA sequence in an ancestral tandem duplication

1989 ◽  
Vol 9 (10) ◽  
pp. 4416-4421
Author(s):  
W S Grayburn ◽  
E U Selker
Keyword(s):  
Dna Methylation ◽  
Tandem Duplication ◽  
De Novo ◽  
5S Rrna ◽  
Rrna Genes ◽  
Structural Basis ◽  
Rrna Gene ◽  
Oak Ridge ◽  
5S Rrna Gene ◽  
5S Rrna Genes

5S rRNA genes of Neurospora crassa are generally dispersed in the genome and are unmethylated. The xi-eta region of Oak Ridge strains represents an informative exception. Most of the cytosines in this region, which consists of a diverged tandem duplication of a 0.8-kilobase-pair segment including a 5S rRNA gene, appear to be methylated (E. U. Selker and J. N. Stevens, Proc. Natl. Acad. Sci. USA 82:8114-8118, 1985). Previous work demonstrated that the xi-eta region functions as a portable signal for de novo DNA methylation (E. U. Selker and J. N. Stevens, Mol. Cell. Biol. 7:1032-1038, 1987; E. U. Selker, B. C. Jensen, and G. A. Richardson, Science 238:48-53, 1987). To identify the structural basis of this property, we have isolated and characterized an unmethylated allele of the xi-eta region from N. crassa Abbott 4. The Abbott 4 allele includes a single 5S rRNA gene, theta, which is different from all previously identified Neurospora 5S rRNA genes. Sequence analysis suggests that the xi-eta region arose from the theta region by duplication of a 794-base-pair segment followed by 267 G.C to A.T mutations in the duplicated DNA. The distribution of these mutations is not random. We propose that the RIP process of N. crassa (E. U. Selker, E. B. Cambareri, B. C. Jensen, and K. R. Haack, Cell 51:741-752, 1987; E. U. Selker, and P. W. Garrett, Proc. Natl. Acad. Sci. USA 85:6870-6874, 1988; E. B. Cambareri, B. C. Jensen, E. Schabtach, and E. U. Selker, Science 244:1571-1575, 1989) is responsible for the numerous transition mutations and DNA methylation in the xi-eta region. A long homopurine-homopyrimidine stretch immediately following the duplicated segment is 9 base pairs longer in the Oak Ridge allele than in the Abbott 4 allele. Triplex DNA, known to occur in homopurine-homopyrimidine sequences, may have mediated the tandem duplication.

scholarly journals Draft genome assembly data of Anoxybacillus sp. strain MB8 isolated from Tattapani hot springs, India

2021 ◽  
Author(s):  
VISHNU PRASOODANAN P K ◽  
Shruti S. Menon ◽  
Rituja Saxena ◽  
Prashant Waiker ◽  
Vineet K Sharma
Keyword(s):  
Hot Springs ◽  
De Novo ◽  
Draft Genome ◽  
Gc Content ◽  
Central India ◽  
Glycoside Hydrolases ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Protein Coding ◽  
Protein Coding Genes

Discovery of novel thermophiles has shown promising applications in the field of biotechnology. Due to their thermal stability, they can survive the harsh processes in the industries, which make them important to be characterized and studied. Members of Anoxybacillus are alkaline tolerant thermophiles and have been extensively isolated from manure, dairy-processed plants, and geothermal hot springs. This article reports the assembled data of an aerobic bacterium Anoxybacillus sp. strain MB8, isolated from the Tattapani hot springs in Central India, where the 16S rRNA gene shares an identity of 97% (99% coverage) with Anoxybacillus kamchatkensis strain G10. The de novo assembly and annotation performed on the genome of Anoxybacillus sp. strain MB8 comprises of 2,898,780 bp (in 190 contigs) with a GC content of 41.8% and includes 2,976 protein-coding genes,1 rRNA operon, 73 tRNAs, 1 tm-RNA and 10 CRISPR arrays. The predicted protein-coding genes have been classified into 21 eggNOG categories. The KEGG Automated Annotation Server (KAAS) analysis indicated the presence of assimilatory sulfate reduction pathway, nitrate reducing pathway, and genes for glycoside hydrolases (GHs) and glycoside transferase (GTs). GHs and GTs hold widespread applications, in the baking and food industry for bread manufacturing, and in the paper, detergent and cosmetic industry. Hence, Anoxybacillus sp. strain MB8 holds the potential to be screened and characterized for such commercially relevant enzymes.

scholarly journals Cydrasil 3, a curated 16S rRNA gene reference package and web app for cyanobacterial phylogenetic placement

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Daniel Roush ◽  
Ana Giraldo-Silva ◽  
Ferran Garcia-Pichel
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Web Application ◽  
De Novo ◽  
Reference Sequence ◽  
Rrna Gene ◽  
Automated Classification ◽  
Reference Tree ◽  
Phylogenetic Placement ◽  
Routine Identification

AbstractCyanobacteria are a widespread and important bacterial phylum, responsible for a significant portion of global carbon and nitrogen fixation. Unfortunately, reliable and accurate automated classification of cyanobacterial 16S rRNA gene sequences is muddled by conflicting systematic frameworks, inconsistent taxonomic definitions (including the phylum itself), and database errors. To address this, we introduce Cydrasil 3 (https://www.cydrasil.org), a curated 16S rRNA gene reference package, database, and web application designed to provide a full phylogenetic perspective for cyanobacterial systematics and routine identification. Cydrasil 3 contains over 1300 manually curated sequences longer than 1100 base pairs and can be used for phylogenetic placement or as a reference sequence set for de novo phylogenetic reconstructions. The web application (utilizing PaPaRA and EPA-ng) can place thousands of sequences into the reference tree and has detailed instructions on how to analyze results. While the Cydrasil web application offers no taxonomic assignments, it instead provides phylogenetic placement, as well as a searchable database with curation notes and metadata, and a mechanism for community feedback.

scholarly journals A de novo approach to disentangle partner identity and function in holobiont systems

2017 ◽  
Author(s):  
Arnaud Meng ◽  
Camille Marchet ◽  
Erwan Corre ◽  
Pierre Peterlongo ◽  
Adriana Alberti ◽  
...  
Keyword(s):  
Functional Diversity ◽  
De Novo ◽  
Model Organisms ◽  
Symbiotic Association ◽  
Proof Of Concept ◽  
Short Read ◽  
Symbiotic Associations ◽  
Functional Annotations ◽  
And Function ◽  
Similarity Method

AbstractBackgroundStudy of meta-transcriptomic datasets involving non-model organisms represents bioinformatic challenges. The production of chimeric sequences and our inability to distinguish the taxonomic origins of the sequences produced are inherent and recurrent difficulties in de novo assembly analyses. The study of holobiont transcriptomes shares similarities with meta-transcriptomic, and hence, is also affected by challenges invoked above. Here we propose an innovative approach to tackle such difficulties which was applied to the study of marine holobiont models as a proof of concept.ResultsWe considered three holobionts models, of which two transcriptomes were previously assembled and published, and a yet unpublished transcriptome, to analyze their raw reads and assign them to the host and/or to the symbiont(s) using Short Read Connector, a k-mer based similarity method. We were able to define four distinct categories of reads for each holobiont transcriptome: host reads, symbiont reads, shared reads and unassigned reads. The result of the independent assemblies for each category within a transcriptome led to a significant diminution of de novo assembled chimeras compared to classical assembly methods. Combining independent functional and taxonomic annotations of each partner’s transcriptome is particularly convenient to explore the functional diversity of an holobiont. Finally, our strategy allowed to propose new functional annotations for two well-studied holobionts and a first transcriptome from a planktonic Radiolaria-Dinophyta system forming widespread symbiotic association for which our knowledge is limited. ConclusionsIn contrast to classical assembly approaches, our bioinformatic strategy not only allows biologists to studying separately host and symbiont data from a holobiont mixture, but also generates improved transcriptome assemblies. The use of Short Read Connector has proven to be an effective way to tackle meta-transcriptomic challenges to study holobiont systems composed of either well-studied or poorly characterized symbiotic lineages such as the newly sequenced marine plankton Radiolaria-Dinophyta symbiosis and ultimately expand our knowledge about these marine symbiotic associations.

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