Phytoplasmas that infect gramineous plants, including Napier grass stunt, sugarcane whiteleaf, sugarcane grassy shoot, and Bermuda grass whiteleaf, have been classified into two closely related groups, 16SrXI and 16SrXIV, based on the 16S ribosomal RNA (rRNA) gene. Subsequently, phytoplasmas associated with coconut and Areca palm in southern India and Sri Lanka have been added into the 16SrXI group. However, the 16S rRNA gene gives relatively poor resolution between these phytoplasmas. In this study, a new set of universal phytoplasma primers that amplify approximately 1 kb of the leucyl transfer RNA synthetase (leuS) gene have been validated on a broad range of phytoplasma taxonomic groups. These have been used along with partial sequences of the secA gene to clarify the taxonomic classification of 16SrXI and 16SrXIV phytoplasmas. Based on this data, the sugarcane whiteleaf and grassy shoot phytoplasmas appear to be the same phytoplasma. The Napier grass stunt phytoplasma forms a distinct group from the Bermuda grass whiteleaf and sugarcane phytoplasmas, suggesting that Napier grass stunt should be in its own ‘Candidatus Phytoplasma sp.’. The phytoplasmas associated with coconut and arecanut in southern India and Sri Lanka, which are in the same 16SrXI group, appear in different groups based on secA analysis.

Recently, strategies for controlling Fusarium oxysporum f. sp. lycopersici (Fol), the causal agent of Fusarium wilt of tomato, focus on using effective biocontrol agents. In this study, an analysis of the biocontrol and plant growth promoting (PGP) attributes of 11 isolates of loamy soil Bacillus spp. has been conducted. Among them, the isolates B.PNR1 and B.PNR2 inhibited the mycelial growth of Fol by inducing abnormal fungal cell wall structures and cell wall collapse. Moreover, broad-spectrum activity against four other plant pathogenic fungi, F. oxysporum f. sp. cubense race 1 (Foc), Sclerotium rolfsii, Colletotrichum musae, and C. gloeosporioides were noted for these isolates. These two Bacillus isolates produced indole acetic acid, phosphate solubilization enzymes, and amylolytic and cellulolytic enzymes. In the pot experiment, the culture filtrate from B.PNR1 showed greater inhibition of the fungal pathogens and significantly promoted the growth of tomato plants more than those of the other treatments. Isolate B.PNR1, the best biocontrol and PGP, was identified as Bacillus stercoris by its 16S rRNA gene sequence and whole genome sequencing analysis (WGS). The WGS, through genome mining, confirmed that the B.PNR1 genome contained genes/gene cluster of a nonribosomal peptide synthetase/polyketide synthase, such as fengycin, surfactin, bacillaene, subtilosin A, bacilysin, and bacillibactin, which are involved in antagonistic and PGP activities. Therefore, our finding demonstrates the effectiveness of B. stercoris strain B.PNR1 as an antagonist and for plant growth promotion, highlighting the use of this microorganism as a biocontrol agent against the Fusarium wilt pathogen and PGP abilities in tomatoes.

Phytoplasmas are bacterial plant pathogens with devastating impact on agricultural production worldwide. In eastern Africa, Napier grass stunt disease causes serious economic losses in the smallholder dairy industry. This draft genome sequence of “ Candidatus Phytoplasma oryzae” strain Mbita1 provides insight into its genomic organization and the molecular basis of pathogenicity.

Thirty isolates of Streptomyces like colony isolated from vermicompost soils were assessed for their antagonistic and plant growth-promoting (PGP) activities. Five isolates having the best inhibitory activity against five plant pathogenic fungi, Colletotrichum gloeosporioides, C. musae, Fusarium sp. TFPK201, Fusarium sp. Foc 1699 and Pestalotia sp. were subsequently identified by 16S rDNA analysis. The selected isolates were classified in the genus Streptomyces and given the name of Streptomyces spp. SEF1, SEF8, SEF47, SEF48 and SEF49, respectively. Then, their PGP and antifungal activities were evaluated. The results showed that the selected isolates were able to produce IAA, siderophore, and amylase. Production of IAA was ranged from 14.06 to 16.59 µg/mL. The highest siderophore production was found in the isolate SEF48. Only isolates SEF47, SEF48, and SEF49 showed amylolytic activity. The culture filtrate from the tested Streptomyces spp. inhibited the fungal mycelial growth and suppressed conidial germination, but their inhibition ability was different. Interestingly, the application of all selected culture filtrates before disease infection significantly decreased tomato Fusarium wilt disease incidence and severity. However, only Streptomyces sp. SEF47 could significantly reduce the disease incidence and severity when it was applied after the disease infection. Moreover, this research found the plant growth-promoting ability of the culture filtrate of selected isolates on tested tomatoes. The Streptomyces sp. SEF47 provided a significant ability for controlling all tested plant pathogenic fungi and promoting plant growth. Therefore, Streptomyces sp. SEF47 could be considerable biocontrol and PGP agent used in sustainable agriculture.