Rhizosphere microbiome metagenomics of gray mangroves (Avicennia marina) in the Red Sea

Alzubaidy, Hanin S.; Essack, Magbubah; Malas, Tareq B.; Bokhari, Ameerah; Motwalli, Olaa; Kamanu, Frederick; Jamhor, Suhaiza; Mokhtar, Noor Azlin; Antunes, André; Simões, Marta Filipa; Álam, Intikhab; Bougouffa, Salim; Lafi, Feras F.; Bajic, Vladimir B.; Archer, John

doi:10.1016/j.gene.2015.10.032

Cited by 122 publications

(87 citation statements)

References 58 publications

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“…A recent metagenomics study reported the microbiome that inhabits the gray mangroves rhizosphere from the Red Sea, are in close proximity (Thuwal, Saudi Arabia) to the mangroves researched in this study (Alzubaidy et al, 2016). This mangrove located in Thuwal represents a pristine mangrove.…”

Section: Microbial Abundance Analysis At the Phylum Levelmentioning

confidence: 55%

“…Thus, we further determined the odds of antibiotic biosynthesis activity occurring in the phyla of interest compared to the odds of antibiotic biosynthesis activity occurring in Actinobacteria, represented as the odds ratio in Table 8. The odds ratio was determined for MNK, MNR, Thuwal -mangrove (MNT) (Alzubaidy et al, 2016), Lake Washington -Freshwater lake (LWF) (Wakeham, 1977) and Lake Tyrell -Hypersaline lake (LTHS) (Podell et al, 2014).…”

Section: Production Of Bioactive Secondary Metabolitesmentioning

confidence: 99%

“…However, metagenomics combined with phylogenetic studies reveals that less than 1 % of bacterial diversity has been successfully cultured to date (Amann et al, 1995). Metagenomic approaches have facilitated a more comprehensive and culture-independent description of the microbial populations present in mangroves (Andreote et al, 2012;Xu et al, 2014;Basak et al, 2015;Simoes et al, A C C E P T E D M A N U S C R I P T Alzubaidy et al, 2016) and coastal MM ecosystems (Bauersachs et al, 2011;Bolhuis and Stal, 2011;Armitage et al, 2012). Heterologous cloning and expression of metagenomic samples have been used for functional-based or sequence-based screening (Couto et al, 2010;Ye et al, 2010;Li et al, 2012;Mai et al, 2014;Goncalves et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

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Metagenomics as a preliminary screen for antimicrobial bioprospecting

Al-Amoudi

Razali

Essack

et al. 2016

Gene

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Since the composition of soil directs the diversity of the contained microbiome and its potential to produce bioactive compounds, many studies has been focused on sediment types with unique features characteristic of extreme environments. However, not much is known about the potential of microbiomes that inhabit the highly saline and hot Red Sea lagoons. This case study explores mangrove mud and the microbial mat of sediments collected from the Rabigh harbor lagoon and Al Kharrar lagoon for antimicrobial bioprospecting. Rabigh harbor lagoon appears the better location, and the best sediment type for this purpose is mangrove mud. On the other hand, Al Kharrar lagoon displayed increased anaerobic hydrocarbon degradation and an abundance of bacterial DNA associated with antibiotic resistance. Moreover, our findings show an identical shift in phyla associated with historic hydrocarbon contamination exposure reported in previous studies (that is, enrichment of Gamma- and Delta-proteobacteria), but we also report that bacterial DNA sequences associated with antibiotic synthesis enzymes are derived from Gamma-, Delta- and Alpha-proteobacteria. This suggests that selection pressure associated with hydrocarbon contamination tend to enrich the bacterial classes DNA associated with antibiotic synthesis enzymes. Although Actinobacteria tends to be the common target for research when it comes to antimicrobial bioprospecting, our study suggests that Firmicutes (Bacilli and Clostridia), Bacteroidetes, Cyanobacteria, and Proteobacteria should be antimicrobial bioprospecting targets as well. To the best of our knowledge, this is the first metagenomic study that analyzed the microbiomes in Red Sea lagoons for antimicrobial bioprospecting.

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Section: Microbial Abundance Analysis At the Phylum Levelmentioning

confidence: 55%

Section: Production Of Bioactive Secondary Metabolitesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Metagenomics as a preliminary screen for antimicrobial bioprospecting

Al-Amoudi

Razali

Essack

et al. 2016

Gene

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“…from mangrove plants is already known for producing diverse extracellular enzymes (Dias et al, 2009;Khianngam et al, 2013). Recently, a metagenomic study from Saudi Arabia reported the identification of microbial communities in Red Sea mangrove (Avicennia marina) (Alzubaidy et al, 2016). However, it was not a functional study, unlike the present study.…”

Section: Discussionmentioning

confidence: 72%

Isolation, diversity, and biotechnological potential of rhizo- and endophytic bacteria associated with mangrove plants from Saudi Arabia

Bibi¹,

Ullah²,

Alvi

et al. 2017

Genet. Mol. Res.

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ABSTRACT. Marine bacteria have been exceptional sources of halotolerant enzymes since decades. The aim of the present study was to isolate bacteria producing hydrolytic enzymes from seven different mangroves collected from the coastal area of Thuwal, Jeddah, Saudi Arabia, and to further screen them for other enzymatic and antifungal activities. We have isolated 46 different rhizo-and endophytic bacteria from the soil, roots, and leaves of the mangroves using different enzymatic media. These bacterial strains were capable of producing industrially important enzymes (cellulase, protease, lipase, and amylase). The bacteria were screened further for antagonistic activity against fungal pathogens. Finally, these bacterial strains were identified on the basis of the16S rDNA sequence. Taxonomic and phylogenetic analysis revealed 95.9-100% sequence identity to type strains of related species. The dominant phylum was Gammaproteobacteria (γ-Proteobacteria), which comprised 10 different genera -Erwinia, Vibrio, Psychrobacter, Aidingimonas, Marinobacter, Chromohalobacter, Halomonas, Microbulbifer, and Alteromonas. Firmicutes was the second dominant phylum, which contained only the genus Bacillus. Similarly, only Isoptericola belonged to Actinobacteria. Further these enzymeproducing bacteria were tested for the production of other enzymes. Most of the active strains showed cellulytic and lipolytic activities. Several were also active against fungal pathogens. Our results demonstrated that the mangroves represent an important source of potentially active bacteria producing enzymes and antifungal metabolites (bioactive products). These bacteria are a source of novel halophilic enzymes and antibiotics that can find industrial and medicinal use.

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“…et al (2014) found an enrichment of Type IV Secretion System genes in the rhizosphere of soybean. Similarly, Alzubaidy et al (2016) found a significant higher number of genes linked to Phages, Prophages, Transposable Elements, and Plasmids in the rhizosphere of the mangrove plant Avicennia marina . Together with our results, this evidence suggests that HGT may be a widespread mechanism that facilitates rhizosphere colonization in plants.…”

Section: Discussionmentioning

confidence: 84%

Bacterial Abilities and Adaptation Toward the Rhizosphere Colonization

2016

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The rhizosphere harbors one of the most complex, diverse, and active plant-associated microbial communities. This community can be recruited by the plant host to either supply it with nutrients or to help in the survival under stressful conditions. Although selection for the rhizosphere community is evident, the specific bacterial traits that make them able to colonize this environment are still poorly understood. Thus, here we used a combination of community level physiological profile (CLPP) analysis and 16S rRNA gene quantification and sequencing (coupled with in silico analysis and metagenome prediction), to get insights on bacterial features and processes involved in rhizosphere colonization of sugarcane. CLPP revealed a higher metabolic activity in the rhizosphere compared to bulk soil, and suggested that D-galacturonic acid plays a role in bacterial selection by the plant roots (supported by results of metagenome prediction). Quantification of the 16S rRNA gene confirmed the higher abundance of bacteria in the rhizosphere. Sequence analysis showed that of the 252 classified families sampled, 24 were significantly more abundant in the bulk soil and 29 were more abundant in the rhizosphere. Furthermore, metagenomes predicted from the 16S rRNA gene sequences revealed a significant higher abundance of predicted genes associated with biofilm formation and with horizontal gene transfer (HGT) processes. In sum, this study identified major bacterial groups and their potential abilities to occupy the sugarcane rhizosphere, and indicated that polygalacturonase activity and HGT events may be important features for rhizosphere colonization.

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Rhizosphere microbiome metagenomics of gray mangroves (Avicennia marina) in the Red Sea

Cited by 122 publications

References 58 publications

Metagenomics as a preliminary screen for antimicrobial bioprospecting

Metagenomics as a preliminary screen for antimicrobial bioprospecting

Isolation, diversity, and biotechnological potential of rhizo- and endophytic bacteria associated with mangrove plants from Saudi Arabia

Bacterial Abilities and Adaptation Toward the Rhizosphere Colonization

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