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1.
ISME Commun ; 3(1): 55, 2023 Jun 06.
Artigo em Inglês | MEDLINE | ID: mdl-37280348

RESUMO

The Johor Strait separates the island of Singapore from Peninsular Malaysia. A 1-kilometer causeway built in the early 1920s in the middle of the strait effectively blocks water flowing to/from either side, resulting in low water turnover rates and build-up of nutrients in the inner Strait. We have previously shown that short-term rather than seasonal environmental changes influence microbial community composition in the Johor Strait. Here, we present a temporally-intensive study that uncovers the factors keeping the microbial populations in check. We sampled the surface water at four sites in the inner Eastern Johor Strait every other day for two months, while measuring various water quality parameters, and analysed 16S amplicon sequences and flow-cytometric counts. We discovered that microbial community succession revolves around a common stable state resulting from frequent pulse disturbances. Among these, sporadic riverine freshwater input and regular tidal currents influence bottom-up controls including the availability of the limiting nutrient nitrogen and its biological release in readily available forms. From the top-down, marine viruses and predatory bacteria limit the proliferation of microbes in the water. Harmful algal blooms, which have been observed historically in these waters, may occur only when there are simultaneous gaps in the top-down and bottom-up controls. This study gains insight into complex interactions between multiple factors contributing to a low-resistance but high-resilience microbial community and speculate about rare events that could lead to the occurrence of an algal bloom.

2.
Viruses ; 14(4)2022 03 28.
Artigo em Inglês | MEDLINE | ID: mdl-35458432

RESUMO

Massive amounts of data from nucleic acid sequencing have changed our perspective about diversity and dynamics of marine viral communities. Here, we summarize recent metatranscriptomic and metaviromic studies targeting predominantly RNA viral communities. The analysis of RNA viromes reaffirms the abundance of lytic (+) ssRNA viruses of the order Picornavirales, but also reveals other (+) ssRNA viruses, including RNA bacteriophages, as important constituents of extracellular RNA viral communities. Sequencing of dsRNA suggests unknown diversity of dsRNA viruses. Environmental metatranscriptomes capture the dynamics of ssDNA, dsDNA, ssRNA, and dsRNA viruses simultaneously, unravelling the full complexity of viral dynamics in the marine environment. RNA viruses are prevalent in large size fractions of environmental metatranscriptomes, actively infect marine unicellular eukaryotes larger than 3 µm, and can outnumber bacteriophages during phytoplankton blooms. DNA and RNA viruses change abundance on hourly timescales, implying viral control on a daily temporal basis. Metatranscriptomes of cultured protists host a diverse community of ssRNA and dsRNA viruses, often with multipartite genomes and possibly persistent intracellular lifestyles. We posit that RNA viral communities might be more diverse and complex than formerly anticipated and that the influence they exert on community composition and global carbon flows in aquatic ecosystems may be underestimated.


Assuntos
Ecossistema , Vírus de RNA , Eucariotos/genética , Genoma Viral , Genômica , Filogenia , Vírus de RNA/genética , RNA de Cadeia Dupla , Transcriptoma
3.
Proc Natl Acad Sci U S A ; 116(46): 23299-23308, 2019 11 12.
Artigo em Inglês | MEDLINE | ID: mdl-31659049

RESUMO

The atmosphere is vastly underexplored as a habitable ecosystem for microbial organisms. In this study, we investigated 795 time-resolved metagenomes from tropical air, generating 2.27 terabases of data. Despite only 9 to 17% of the generated sequence data currently being assignable to taxa, the air harbored a microbial diversity that rivals the complexity of other planetary ecosystems. The airborne microbial organisms followed a clear diel cycle, possibly driven by environmental factors. Interday taxonomic diversity exceeded day-to-day and month-to-month variation. Environmental time series revealed the existence of a large core of microbial taxa that remained invariable over 13 mo, thereby underlining the long-term robustness of the airborne community structure. Unlike terrestrial or aquatic environments, where prokaryotes are prevalent, the tropical airborne biomass was dominated by DNA from eukaryotic phyla. Specific fungal and bacterial species were strongly correlated with temperature, humidity, and CO2 concentration, making them suitable biomarkers for studying the bioaerosol dynamics of the atmosphere.


Assuntos
Microbiologia do Ar , Microbiota , Clima Tropical , Poluentes Atmosféricos/análise , Ritmo Circadiano , Ecossistema , Metagenoma , Modelos Biológicos , Singapura
4.
Microbiol Resour Announc ; 8(37)2019 Sep 12.
Artigo em Inglês | MEDLINE | ID: mdl-31515337

RESUMO

The Pontibacter bacterial genus has been detected in marine and soil environments. Here, we report the genome sequence of Pontibacter sp. strain SGAir0037, which was isolated from outdoor air samples collected in Singapore. The genome comprises one chromosome of 5.26 Mb and one plasmid of 127 kb.

5.
Microbiol Resour Announc ; 8(32)2019 Aug 08.
Artigo em Inglês | MEDLINE | ID: mdl-31395634

RESUMO

Nissabacter sp. strain SGAir0207 was isolated from a tropical air sample collected in Singapore. Its genome was assembled using a hybrid approach with long and short reads, resulting in one chromosome of 3.9 Mb and 7 plasmids. The complete genome consists of 4,403 protein-coding, 84 tRNA, and 22 rRNA genes.

6.
Microbiol Resour Announc ; 8(32)2019 Aug 08.
Artigo em Inglês | MEDLINE | ID: mdl-31395637

RESUMO

Agrococcus sp. strain SGAir0287 was isolated from tropical air samples collected in Singapore. Assembled using single-molecule real-time (SMRT) sequencing and MiSeq reads, the genome consists of one circular chromosome of 3,084,767 bp. The entire genome has 2,870 protein-coding genes, 45 tRNAs, and 3 rRNAs.

12.
Microbiol Resour Announc ; 8(34)2019 Aug 22.
Artigo em Inglês | MEDLINE | ID: mdl-31439708

RESUMO

Microbacterium sp. strain SGAir0570 was isolated from air samples collected in Singapore. Its genome was assembled using single-molecule real-time sequencing and MiSeq short reads. It has one chromosome with a length of 3.38 Mb and one 59.2-kb plasmid. It contains 3,170 protein-coding genes, 48 tRNAs, and 6 rRNAs.

13.
Genome Announc ; 6(27)2018 Jul 05.
Artigo em Inglês | MEDLINE | ID: mdl-29976611

RESUMO

The thermophilic bacterium Geobacillus thermoleovorans was isolated from a tropical air sample collected in Singapore. The genome was sequenced on the PacBio RS II platform and consists of one chromosome with 3.6 Mb and one plasmid with 75 kb. The genome comprises 3,509 protein-coding genes, 88 tRNAs, and 27 rRNAs.

14.
Genome Announc ; 6(27)2018 Jul 05.
Artigo em Inglês | MEDLINE | ID: mdl-29976613

RESUMO

Bacillus velezensis strain SGAir0473 (Firmicutes) was isolated from tropical air collected in Singapore. Its genome was assembled using short reads and single-molecule real-time sequencing and comprises one chromosome with 4.18 Mb. The genome consists of 3,937 protein-coding genes, 86 tRNAs, and 27 rRNAs.

15.
Genome Announc ; 6(22)2018 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-29853498

RESUMO

Pseudomonas stutzeri strain SGAir0442 was isolated from tropical air samples collected in Singapore. It is a Gram-negative denitrifying bacterium and an opportunistic human pathogen. Its complete genome consists of one chromosome of 4.52 Mb, containing 4,129 protein-coding genes, 12 rRNA subunits, and 62 tRNAs.

16.
Genome Announc ; 6(18)2018 May 03.
Artigo em Inglês | MEDLINE | ID: mdl-29724826

RESUMO

Lelliottia nimipressuralis type strain SGAir0187 was isolated from tropical air samples collected in Singapore. The genome was assembled with an average coverage of 180-fold using Pacific Biosciences long reads and Illumina MiSeq paired-end reads. The genome measures 4.8 Mb and contains 4,424 protein-coding genes, 83 tRNAs, and 25 rRNAs.

17.
Genome Announc ; 6(18)2018 May 03.
Artigo em Inglês | MEDLINE | ID: mdl-29724855

RESUMO

Acinetobacter indicus (Gammaproteobacteria) is a strict aerobic nonmotile bacterium. The strain SGAir0564 was isolated from air samples collected in Singapore. The complete genome is 3.1 Mb and was assembled using a combination of short and long reads. The genome contains 2,808 protein-coding genes, 80 tRNAs, and 21 rRNA subunits.

18.
Genome Announc ; 6(19)2018 May 10.
Artigo em Inglês | MEDLINE | ID: mdl-29748397

RESUMO

Staphylococcus haemolyticus is a coagulase-negative staphylococcal species that is part of the skin microbiome and an opportunistic human pathogen. The strain SGAir0252 was isolated from tropical air samples collected in Singapore, and its complete genome comprises one chromosome of 2.63 Mb and one plasmid of 41.6 kb.

19.
Genome Announc ; 5(45)2017 Nov 09.
Artigo em Inglês | MEDLINE | ID: mdl-29122878

RESUMO

Bacillus altitudinis strain SGAir0031 (Firmicutes) was isolated from tropical air samples collected in Singapore. Its genome was assembled using short reads and single-molecule real-time sequencing, comprising one chromosome with 3.81 Mb and one plasmid with 32 kb. The genome consists of 3,820 protein-coding genes, 81 tRNAs, and 24 rRNAs.

20.
J Sep Sci ; 39(22): 4299-4304, 2016 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-27662513

RESUMO

The serotype specificity of adenovirus ion-exchange chromatography has previously been studied using standard particle-based columns, and the hexon protein has been reported to determine retention time. In this study, we have submitted Adenovirus type 5 recombinants to anion-exchange chromatography using methacrylate monolithic supports. Our experiments with hexon-modified adenoviral vectors show more precisely that the retention time is affected by the substitution of amino acids in hypervariable region 5, which lies within the hexon DE1 loop. By exploring the recombinants modified in the fiber protein, we have proven the previously predicted chromatographic potential of this surface constituent. Modifications that preserve the net charge of the hexon protein, or those that cause only a small charge difference in the fiber protein, in addition to shortening the fiber shaft, did not change the chromatographic behavior of the adenovirus particles. However, modifications that include the deletion of just two negatively charged amino acids in the hexon protein, or the introduction of a heterologous fiber protein, derived from another serotype, revealed recognizable changes in anion-exchange chromatography. This could be useful in facilitating chromatography-approach purification by creating targeted capsid modifications, thereby shifting adenovirus particles away from particular interfering substances present in the crude lysate.


Assuntos
Adenoviridae , Proteínas do Capsídeo/química , Cromatografia por Troca Iônica , Vetores Genéticos , Substituição de Aminoácidos , Cromatografia Líquida de Alta Pressão
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