Global Genome Comparative Analysis Reveals Insights of Resistome and Life-Style Adaptation of Pseudomonas putida

Most Pseudomonas putida strains are environmental microorganisms exhibiting a wide range of metabolic capability but certain strains have been reported as rare opportunistic pathogens and some emerged as multidrug resistant P. putida. This study aimed to assess the drug resistance profile of, via whole genome analysis, P. putida strain T2-2 isolated from oral cavity. At the same time, we also compared the nonenvironmental strain with environmentally isolated P. putida. In silico comparative genome analysis with available reference strains of P. putida shows that T2-2 has lesser gene counts on carbohydrate and aromatic compounds metabolisms, which suggested its little versatility. The detection of its edd gene also suggested T2-2’s catabolism of glucose via ED pathway instead of EMP pathway. On the other hand, its drug resistance profile was observed via in silico gene prediction and most of the genes found were in agreement with drug-susceptibility testing in laboratory by automated VITEK 2. In addition, the finding of putative genes of multidrug resistance efflux pump and ATP-binding cassette transporters in this strain suggests a multidrug resistant phenotype. In summary, it is believed that multiple metabolic characteristics and drug resistance in P. putida strain T2-2 helped in its survival in human oral cavity

Complete genome sequence of Planococcus donghaensis JH1T, a pectin-degrading bacterium

The type strain Planococcus donghaensis JH1T is a psychrotolerant and halotolerant bacterium with starch-degrading ability. Here, we determine the carbon utilization profile of P. donghaensis JH1T and report the first complete genome of the strain. This study revealed the strain’s ability to utilize pectin and d-galacturonic acid, and identified genes responsible for degradation of the polysaccharides. The genomic information provided may serve as a fundamental resource for full exploration of the biotechnological potential of P. donghaensis JH1T

High Diversity of Bacterial Communities in Developmental Stages of Bactrocera carambolae (Insecta: Tephritidae) Revealed by Illumina MiSeq Sequencing of 16S rRNA Gene

Bactrocera carambolae is a highly polyphagous fruit pest of agricultural importance. This study reports the bacterial communities associated with the developmental stages of B. carambolae. The microbiota of the developmental stages were investigated by targeted 16S rRNA gene (V3–V4 region) sequencing using the Illumina MiSeq. At 97% similarity, there were 19 bacterial phyla and unassigned bacteria, comprising 39 classes, 86 orders, 159 families and 311 genera. The bacterial composition varied among the specimens of developmental stage and across developmental stages as well as exuviae. Four phyla of bacteria (with relative abundance of ≥1% in at least one specimen)—Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria—were recovered from the larva, pupa, adult stages and exuviae. Proteobacteria was the predominant phylum in all the developmental stages as well as the exuviae. Enterobacteriaceae (Proteobacteria) was the predominant family in the adult flies while the family [Weeksellaceae] (Bacteroidetes) was predominant in the larval and pupal stages. Among the genera occurring in more than one developmental stage of B. carambolae, Erwinia was more abundant in the larval stage, Halomonas more abundant in adult female, Stenotrophomonas more abundant in adult male, and Chryseobacterium more abundant in the larval and pupal stages. The results indicate transmission of bacteria OTUs from immatures to the newly emerged adults, and from exuviae to the environment

Predominance of Wolbachia endosymbiont in the microbiota across life stages of Bactrocera latifrons (Insecta: Tephritidae)

The Solanum fruit fly Bactrocera latifrons is an important agricultural pest. There is no report on the microbiota associated with this fruit fly. This study reports the bacterial communities associated with the life stages of this fruit fly from Malaysia. Illumina MiSeq next-generation sequencing of PCR-generated amplicons of 16S rRNA gene revealed the presence of different number of bacterial OTUs in the life stages studied. The number of bacterial OTUs at different taxonomic levels in the larva sample was much higher than in the adult male and adult female samples. The class Alphaproteobacteria of phylum Proteobacteria was predominant across the life stages studied (98.64% in the larva sample, 98.53% in pupa, 97.66% in adult male, and 99.89% in adult female). At the specific level, Wolbachia endosymbiont of Culex quinquefasciatus Pel was detected in all the life stages studied – 98.61% in the larva sample, 98.18% in pupa, 97.59% in adult male, and 99.88% in adult female. The ubiquitous presence of Wolbachia infections across life stages provides evidence for transmission from the larva stage to emerging adults. The role(s) of Wolbachia in B. latifrons remain to be determined

Microbiota associated with Bactrocera carambolae and B. dorsalis (Insecta: Tephritidae) revealed by next-generation sequencing of 16S rRNA gene

Many fruit flies in the genus Bactrocera are agricultural pests. The microbiota associated with these insects may provide beneficial services to their hosts. This study reports the microbiota associated with Bactrocera carambolae and B. dorsalis from Malaysia, of which B. carambolae represents the first report. Six mature adult male Bactrocera specimens were collected in Peninsular Malaysia and whole genome DNA of individual specimen was extracted. The microbiotas of these specimens were investigated using targeted 16S rRNA gene (V3 region) sequencing using the Illumina MiSeq. Next-generation sequencing of the 16S rRNA gene revealed the presence of 6 bacterial phyla (Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, Proteobacteria, Tenericutes) in both B. carambolae and B. dorsalis, Fusobacteria in B. carambolae and Planctomycetes in B. dorsalis. The bacterial composition varied among conspecific and interspecific fruit fly samples. Proteobacteria was the predominant phylum in all the B. carambolae and B. dorsalis samples. The other major phyla present in all the samples were Actinobacteria, Bacteroidetes and Firmicutes, while three phyla occurred with very low relative abundance (Fusobacteria and Tenericutes sporadically in B. carambolae; and Planctomycetes and Tenericutes in both B. dorsalis samples). For conspecific samples of B. carambolae and B. dorsalis, those from Batu Pahat had higher number of bacterial families, genera and species than those from the University of Malaya. In the present study, 5 bacterial phyla, 10 classes, 20 orders, 30 families, 30 genera and 8 species were identified in all the B. carambolae and B. dorsalis samples. Next-generation sequencing method will greatly facilitate the study of microbial diversity

Microbiota and potential opportunistic pathogens associated with male and female fruit flies of Malaysian Bactrocera carambolae (Insecta: Tephritidae)

Bactrocera carambolae Drew & Hancock is an agricultural pest that causes considerable damage to various fruit crops in Southeast Asia and South America. We report here the bacterial communities associated with field-caught male and female adult flies from University Malaya campus. The microbiota was determined by targeted 16S rRNA gene (V3–V4 region) sequencing using the Illumina MiSeq. At 97% similarity, four bacterial phyla (with relative abundance of ≥1% in at least one specimen) – Bacteroidetes, Firmicutes, Proteobacteria, and Tenericutes – were recovered from the adult flies. Proteobacteria was the predominant phylum in all the samples, with the female flies (86.81 ± 6.57%) having higher mean relative abundance than the male flies (71.57 ± 18.37%). The Firmicutes was more abundant in the male flies (14.47 ± 17.30%) than female flies (0.69 ± 1.25%). There were in total seven classes, nine orders, 13 families, 23 genera, and 31 putative species. Thirteen genera had higher mean relative abundance in male flies, and nine in female flies. Klebsiella was the predominant genus in female flies, while Desulfovibrio was more abundant in some male flies. The mean relative abundances of the putative species Orbus sasakiae and Enterococcus moraviensis were significantly higher in male than female flies, while female flies had significantly higher mean relative abundance for Escherichia fergusonii and Klebsiella variicola. Alpha diversity indices indicated that the bacterial diversity varied within and between male and female flies, and the mean bacterial diversity was significantly higher in male flies. The differences in bacterial diversity and relative abundance may be reasonably attributed to stochastic processes, in part to environmental factors such as food resources and habitats. It is significant that several putative bacterial species recovered in the present study have not been reported in Bactrocera fruit flies. Sixteen of the 31 detected putative bacterial species are potential opportunistic pathogens of medical/public health importance

Arbuscular Mycorrhizal Symbiosis: A Strategy for Mitigating the Impacts of Climate Change on Tropical Legume Crops

Climate change is likely to have severe impacts on food security in the topics as these regions of the world have both the highest human populations and narrower climatic niches, which reduce the diversity of suitable crops. Legume crops are of particular importance to food security, supplying dietary protein for humans both directly and in their use for feed and forage. Other than the rhizobia associated with legumes, soil microbes, in particular arbuscular mycorrhizal fungi (AMF), can mitigate the effects of biotic and abiotic stresses, offering an important complementary measure to protect crop yields. This review presents current knowledge on AMF, highlights their beneficial role, and explores the potential for application of AMF in mitigating abiotic and biotic challenges for tropical legumes. Due to the relatively little study on tropical legume species compared to their temperate growing counterparts, much further research is needed to determine how similar AMF–plant interactions are in tropical legumes, which AMF species are optimal for agricultural deployment and especially to identify anaerobic AMF species that could be used to mitigate flood stress in tropical legume crop farming. These opportunities for research also require international cooperation and support, to realize the promise of tropical legume crops to contribute to future food security

A halotolerant plant growth promoting consortium of Bacillus sp. RB3 and Pseudomonas sp. EB3 primes banana, Musa acuminata cv. Berangan, against salinity and Foc-TR4 stresses

A plant-growth promoting bacterial consortium of halotolerant Bacillus sp. and Pseudomonas sp. was evaluated for the ability to prime banana (Musa acuminata cv. Berangan) plants against abiotic (salinity) and biotic (Foc-TR4) stress challenges. PGPB consortium-primed banana plants showed better growth (plant height, root length and root biomass) and improved physiological parameters (relative water content, chlorophyll, and carotenoid contents) in both stressed conditions compared to non-primed banana plants. In addition, primed banana plants showed a reduction in lipid peroxidation and an increase in proline and antioxidant enzymatic activities (superoxide dismutase, catalase, ascorbate peroxidase, peroxidase, and glutathione reductase). In salt-stress conditions (sea salt at 100 mM NaCl equivalent), primed plants showed higher levels of K+, Ca2+, and Mg2+ and lower levels of Cl- and Na+ compared to non-primed salt-stressed plants. Under Foc-TR4 stress, the primed plants showed significant enhancement in the levels of total soluble phenolics, lignin content and defense-related enzyme activities (β-1, 3-glucanase, phenylalanine ammonia lyase, chitinase, polyphenol oxidase, and lipoxygenase). Expression analysis of nine stress-responsive MaWRKY genes (MaWRKY4, MaWRKY23, MaWRKY24, MaWRKY25, MaWRKY28, MaWRKY45, MaWRKY65, MaWRKY89 and MaWRKY145) showed significant upregulation in primed banana plants under salt and Foc-TR4 stresses compared to non-primed plants. These results demonstrate that inoculation with the PGPB consortium improved banana plant growth characteristics and primed WRKY-mediated protection against abiotic and biotic stresses

Core members and differential abundance of chrysomelid microbiota in the life stages of Podontia affinis (Galerucinae) and adult Silana farinosa (Cassidinae, Coleoptera)

The chrysomelid beetles Podontia affinis and Silana farinosa are members of the subfamilies Galerucinae and Cassidinae, respectively. This study, based on 16S rRNA gene-targeted metagenomics sequencing, reports the core members and differential abundance of bacterial communities in the larvae and adult beetles of P. affinis and the adult S. farinosa. Cyanobacteria/Melainabacteria group was the predominant phylum in the larvae of P. affinis, while Proteobacteria was the predominant phylum in adult P. affinis and S. farinosa. The number of Order, Family, Genus and Species OTUs in the adult stage of P. affinis was higher than that in the larval stage. The bacterial species richness of adult P. affinis was significantly higher than that of adult S. farinosa. Betaproteobacteria was the predominant class in adult P. affinis, Cyanobacteria in the larvae of P. affinis and Gammaproteobacteria in S. farinosa. The larvae and adult beetles of P. affinis and adult S. farinosa had a low number of unique and shared bacterial OTUs (> 5% relative abundance). The differences in the microbiota indicate possible differences in nutrient assimilation, host taxonomy and other stochastic processes. These findings provide new information to our understanding of the bacteria associated with specialist phytophagous chrysomelid beetles and beetles in general