Novel multifunctional plant growth–promoting bacteria in co-compost of palm oil industry waste

Novel multifunctional plant growth-promoting bacteria isolated from the oil palm rhizosphere under long-term organic matter application

Most agricultural products are presently cultivated on marginal lands with poor soil properties and unfavorable environmental conditions (diseases and abiotic stresses), which can threaten plant growth and yield. Plant growth-promoting bacteria (PGPB) are beneficial bacteria that promote plant growth and biomass and act as biocontrols against diseases and stress. However, most isolated PGPBs have a single function and low survival rates owing to their limited growth behaviors. In this study, we isolated multifunctional PGPB from oil palm rhizosphere, quantitatively measured their activities, and evaluated their effectiveness in Brassica rapa (Komatsuna) cultivation. This is the first study to report the isolation of three multifunctional PGPB strains with ammonium production, phosphate-potassium-silicate solubilization, and indole-3-acetic acid (IAA) production from the oil palm rhizosphere, namely Kosakonia oryzendophytica AJLB38, Enterobacter quasimori AJTS77, and Lelliottia jeotgali AJTS83. Additionally, these strains showed antifungal activity against the oil palm pathogen Ganoderma boninense. These strains grow under high temperature, acidic and alkaline pH, and high salt concentration, which would result in their proliferation in various environmental conditions. The cultivation experiments revealed these strains improved the growth and biomass with half the dosage of chemical fertilizer application, which was not significantly different to the full dosage. Furthermore, the overall plant growth-promoting activities in quantitative assays and overall B. rapa growth in cultivation experiments were statistically correlated, which could contribute to the prediction of plant growth promotion without plant cultivation experiments. Thus, the selected PGPB could be valuable as a biofertilizer to improve soil health and quality and promote agricultural sustainability.

Food waste-based bio-fertilizers production by bio-based fermenters and their potential impact on the environment

Increasing food waste is creating a global waste (and management) crisis. Globally, ∼1.6 billion tons of food is wasted annually, worth ∼$1.2 trillion. By reducing this waste or by turning it into valuable products, numerous economic advantages can be realized, including improved food security, lower production costs, biodegradable products, environmental sustainability, and cleaner solutions to the growing world's waste and garbage management. The appropriate handling of these detrimental materials can significantly reduce the risks to human health. Food waste is available in biodegradable forms and, with the potential to speed up microbial metabolism effectively, has immense potential in improving bio-based fertilizer generation. Synthetic inorganic fertilizers severely affect human health, the environment, and soil fertility, thus requiring immediate consideration. To address these problems, agricultural farming is moving towards manufacturing bio-based fertilizers via utilizing natural bioresources. Food waste-based bio-fertilizers could help increase yields, nutrients, and organic matter and mitigate synthetic fertilizers' adverse effects. These are presented and discussed in the review.

Different traits for cold tolerance of extremely thermophilic Calditerricola strains isolated from mesothermal municipal sewage sludge and its hyperthermal compost

Extreme thermophiles Calditerricola satsumensis DD2 and D3 were isolated from mesothermal municipal sludge, a material used for hyperthermal composting. To understand the ecologically anomalous findings, their behavior at various temperatures, membrane fatty acid composition, and draft genome sequences were compared with those of C. satsumensis YMO81T and Calditerricola yamamurae YMO722T, already isolated from hyperthermal compost. All four strains grew between 56 and 83 °C. However, strains DD2 and D3 were stable for ≥48 h at a wide range of temperatures (20-75 °C), while strains YMO81T and YMO722T were highly labile at lower temperatures. The former strains maintained their colony-forming ability for >180 days at 20 °C, while the latter strains lost it within 1 d. All four strains showed similar composition of membrane fatty acid, which were not affected by 20 °C treatment. Comparative draft genome analyses showed that 13 candidate genes were present only in strains DD2 and D3, and the specific expression of six gene homologs was confirmed. A DNA chaperone, site-specific recombinase XerD homolog, had tetra adenine sequence at its upper gene region, and was up-regulated by 20 °C treatment in DD2 and D3, suggesting a possible role in the cold tolerance of sludge-derived strains. In addition, the lack of another possible DNA chaperone, a homolog of the ATP-dependent DNA helicase, in the compost-derived strains may accelerate their sensitivity to cold shock. In conclusion, we speculate that the specific phenotypic and genotypic characteristics of sludge-derived strains are responsible for their unusual ecological distribution at ambient temperatures.

Exploring the potential of Bornean polypore fungi as biological control agents against pathogenic Ganoderma boninense causing basal stem rot in oil palm

Basal stem rot due to a fungal pathogen, Ganoderma boninense, is one of the most devastating diseases in oil palm throughout the major palm oil producer countries. This study investigated the potential of polypore fungi as biological control agents against pathogenic G. boninense in oil palm. In vitro antagonistic screening of selected non-pathogenic polypore fungi was performed. Based on in planta fungi inoculation on oil palm seedlings, eight of the 21 fungi isolates tested (GL01, GL01, RDC06, RDC24, SRP11, SRP12, SRP17, and SRP18) were non-pathogenic. In vitro antagonistic assays against G. boninense revealed that the percentage inhibition of radial growth (PIRG) in dual culture assay for SRP11 (69.7%), SRP17 (67.3%), and SRP18 (72.7%) was relatively high. Percentage inhibition of diameter growth (PIDG) in volatile organic compounds (VOCs) in dual plate assay of SRP11, SRP17, and SRP18 isolates were 43.2%, 51.6%, and 52.1%, respectively. Molecular identification using the internal transcribed spacer gene sequences of SRP11, SRP17, and SRP18 isolates revealed that they were Fomes sp., Trametes elegans, and Trametes lactinea, respectively.

Changes in the microbiota during biological treatment of palm oil mill waste: A critical review

Palm oil mill waste has a complex cellulosic structure, is rich in nutrients, and provides a habitat for diverse microbial communities. Current research focuses on how the microbiota and organic components interact during the degradation of this type of waste. Some recent studies have described the microbial communities present in different biodegradation processes of palm oil mill waste, identifying the dominant bacteria/fungi responsible for breaking down the cellulosic components. However, understanding the degradation process's mechanisms is vital to eliminating the need for further pretreatment of lignocellulosic compounds in the waste mixture and facilitating the commercialization of palm oil mill waste treatment technology. Thus, the present work aims to review microbial community dynamics via three biological treatment systems comprehensively: composting, vermicomposting, and dark fermentation, to understand how inspiration from nature can further enhance existing degradation processes. The information presented could be used as an umbrella to current research on biological treatment processes and specific research on the bioaugmentation of indigenous microbial consortia isolated during the biological degradation of palm oil mill waste.

Compost-derived indole-3-acetic-acid-producing bacteria and their effects on enhancing the secondary fermentation of a swine manure-corn stalk composting

Composting, as an effectively bio-oxidative process, has been widely used for converting organic waste to organic fertilizer. However, the low fertilizer efficiency of composting product limited its application in agriculture. To improve the growth-promoting effect of composting product, the present study investigated the bioaugmentation strategy of inoculating indole-3-acetic-acid (IAA)-producing bacteria. Firstly, two IAA-producing bacteria (Bacillus safensis 33C and Rhodococcus rhodochrous YZ) were isolated from composting products with high IAA yields of 39.18 and 16.32 μg mL^-1, respectively. Secondly, the microbial inoculants were prepared with 33C, YZ and a previously isolated IAA-producing strain Corynebacterium stationis 29B. To increase the accumulation of microbial secondary metabolites, microbial inoculants were amended at the secondary fermentation stage of composting. Physicochemical characterization showed that the maturity of composting product was significantly promoted by inoculating microbial inoculants prepared with 33C and 29B (single and combined inoculants). Finally, bioaugmentation with 33C and 29B increased the IAA contents of composting products by 2.9-5.2 times, which benefited the germination and early vegetative growth of plants. In summary, inoculating proper IAA-producing bacteria during secondary fermentation of composting could improve the quality of composting product and expand its application.

Effects of Mixing Garlic Skin on Fermentation Quality, Microbial Community of High-Moisture Pennisetum hydridum Silage

Garlic skin, a by-product of garlic processing, was supposed to improve the fermentation quality of high-moisture silages because of its low moisture content and active compounds. Thus, fermentation and microbial characteristics of high-moisture Pennisetum hydridum ensiled with the addition of 0, 10, 20, and 30 wt% garlic skin (on a fresh matter basis) were analyzed during a 60-days fermentation. Results showed that the addition of garlic skin increased the dry matter content and lactic acid production, and decreased the pH and ammonia-N content of the silage. Adding garlic skin changed the relative abundance of bacterial communities with an increase in Lactobacillus and a decrease in Clostridium relative abundance. In conclusion, co-ensiling of high-moisture Pennisetum hydridum with garlic skin could be a simple approach to improve the silage quality and nutrients preservation.

Effects of different microbial pretreatments on the anaerobic digestion of giant grass under anaerobic and microaerobic conditions

Microbial pretreatment to lignocellulosic biomass for anaerobic digestion (AD) has achieved increased attention; however, the low efficiency and unclear mechanism of oxygen parameter affecting this process performance limit its practical application. In this study, five readily available microbial consortia were developed to analyze the influences of various oxygen concentrations during pretreatment process upon methane conversion efficiency and microbiota within AD of giant grass. Results found that anaerobic pretreatment by liquid or straw composting inoculant, along with microaerobic pretreatment by cow manure at 10 mL/g VS oxygen concentration, obtained 23.1%, 24.4%, and 16.0% higher methane yields (275.3, 279.8, and 265.3 mL/g VS) than corresponding untreated group, respectively. Microbial community analyses showed that microbial responses to oxygen varied significantly with microbial consortium, which consequently caused different AD performances. The findings will enrich theoretical knowledge of microbial pretreatment and provide a technological guidance for efficient utilization of giant grass and other lignocellulosic biomasses.

Thermo-resistant enzyme-producing microorganisms isolated from composting

Organo-mineral fertilizers supplemented with biological additives are an alternative to chemical fertilizers. In this study, thermoresistant microorganisms from composting mass were isolated by two-step procedures. First, samples taken at different time points and temperatures (33 days at 52 ºC, 60 days at 63 ºC, and over 365 days at 26 ºC) were pre-incubated at 80 oC for 30 minutes. Second, the microbial selection by in vitro culture-based methods and heat shock at 60 oC and 100 oC for 2h and 4h. Forty-one isolates were able to grow at 60 °C for 4h; twenty-seven at 100 °C for 2h, and two at 100 °C for 4h. The molecular identification by partial sequencing of the 16S ribosomal gene using universal primers revealed that thirty-five isolates were from eight Bacillus species, one Brevibacillus borstelensis, three Streptomyces thermogriseus, and two fungi (Thermomyces lanuginosus and T. dupontii). Data from amylase, phytase, and cellulase activity assays and the enzymatic index (EI) showed that 38 of 41 thermo-resistant isolates produce at least one enzyme. For amylase activity, the highest EI value was observed in Bacillus licheniformis (isolate 21C2, EI= 4.11), followed by Brevibacillus borstelensis (isolate 6C2, EI= 3.66), Bacillus cereus (isolate 18C2, EI= 3.52), and Bacillus paralicheniformis (isolate 20C2, EI= 3.34). For phytase, the highest EI values were observed for Bacillus cereus (isolate 18C2, EI= 2.30) and Bacillus licheniformis (isolate 3C1, EI= 2.15). Concerning cellulose production, B. altitudinis (isolate 6C1) was the most efficient (EI= 6.40), followed by three Bacillus subtilis (isolates 9C1, 16C2, and 19C2) with EI values of 5.66, 5.84, and 5.88, respectively, and one B. pumilus (isolate 27C2, EI= 5.78). The selected microorganisms are potentially useful as a biological additive in organo-mineral fertilizers and other biotechnological processes.

Development and Application of Low-Cost and Eco-Sustainable Bio-Stimulant Containing a New Plant Growth-Promoting Strain Kosakonia pseudosacchari TL13

The use of beneficial microbes as inoculants able to improve fitness, growth and health of plants also in stress conditions is an attractive low-cost and eco-friendly alternative strategy to harmful chemical inputs. Thirteen potential plant growth-promoting bacteria were isolated from the rhizosphere of wheat plants cultivated under drought stress and nitrogen deficiency. Among these, the two isolates TL8 and TL13 showed multiple plant growth promotion activities as production of indole-3-acetic acid (IAA), siderophores, ammonia, and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase production, the ability to solubilize phosphate as well as exerted antimicrobial activity against plant pathogens as Botrytis spp. and Phytophthora spp. The two selected strains were identified as Kosakonia pseudosacchari by sequencing of 16S rRNA gene. They resulted also tolerant to abiotic stress and were able to efficiently colonize plant roots as observed in vitro assay under fluorescence microscope. Based on the best PGP properties, the strain K. pseudosacchari TL13 was selected to develop a new microbial based formulate. A sustainable and environmentally friendly process for inoculant production was developed using agro-industrial by-products for microbial growth. Moreover, the application of K. pseudosacchari TL13- based formulates in pot experiment improved growth performance of maize plants.

Harnessing the Microbiomes of Suppressive Composts for Plant Protection: From Metagenomes to Beneficial Microorganisms and Reliable Diagnostics

Soil-borne diseases cause significant yield losses worldwide, are difficult to treat and often only limited options for disease management are available. It has long been known that compost amendments, which are routinely applied in organic and integrated farming as a part of good agricultural practice to close nutrient cycles, can convey a protective effect. Yet, the targeted use of composts against soil-borne diseases is hampered by the unpredictability of the efficacy. Several studies have identified and/or isolated beneficial microorganisms (i.e., bacteria, oomycetes, and fungi) from disease suppressive composts capable of suppressing pathogens (e.g., Pythium and Fusarium) in various crops (e.g., tomato, lettuce, and cucumber), and some of them have been developed into commercial products. Yet, there is growing evidence that synthetic or complex microbial consortia can be more effective in controlling diseases than single strains, but the underlying molecular mechanisms are poorly understood. Currently, a major bottleneck concerns the lack of functional assays to identify the most potent beneficial microorganisms and/or key microbial consortia from complex soil and compost microbiomes, which can harbor tens of thousands of species. This focused review describes microorganisms, which have been isolated from, amended to or found to be abundant in disease-suppressive composts and for which a beneficial effect has been documented. We point out opportunities to increasingly harness compost microbiomes for plant protection through an integrated systems approach that combines the power of functional assays to isolate biocontrol and plant growth promoting strains and further prioritize them, with functional genomics approaches that have been successfully applied in other fields of microbiome research. These include detailed metagenomics studies (i.e., amplicon and shotgun sequencing) to achieve a better understanding of the complex system compost and to identify members of taxa enriched in suppressive composts. Whole-genome sequencing and complete assembly of key isolates and their subsequent functional profiling can elucidate the mechanisms of action of biocontrol strains. Integrating the benefits of these approaches will bring the long-term goals of employing microorganisms for a sustainable control of plant pathogens and developing reliable diagnostic assays to assess the suppressiveness of composts within reach.

Fixation of CO2, electron donor and redox microenvironment regulate succinic acid production in Citrobacter amalonaticus

Biological sequestration of CO₂ for generating value added products is an emerging strategy. Succinic acid (SA) is an important C4 building block chemical, and its biological production via CO₂ sequestration, holds many practical applications. This study presents an in-depth insight on SA production using isolated strain belonging to genus Citrobacter, more closely related to Citrobacter amalonaticus by considering critical process parameters such as different carbon sources at various initial concentrations, buffering agent (NaHCO₃) concentrations and different pH conditions. The effect of H₂ gas as an electron donor and availability of CO₂ during SA production was also evaluated. The results from this work demonstrated that the isolated strain depicted the ability to utilize diverse carbon sources and highest SA production was achieved with sucrose as a substrate, indicating that reduced carbon substrates help in maximizing the redox potential. Incorporation of CO₂ and H₂ not only enhanced the production of SA but also affected the total acids profile favoring the production of SA over lactic, formic and acetic acids. Additional supply of CO₂ and H₂ led to maximum SA production of 12.07 gL^-1, productivity of 0.36 gL^-1 h^-1 and SA yield of 48.5%. In control operation when no gases were supplied and in other test conditions where either of the gases were supplied, lactic acid was the major end product followed by acetic acid. The positive effect of CO₂ for SA production provides scope for sustainable integration of SA and the CO₂-generating biofuel industries or industrial side streams.

Aeolian transport of viable microbial life across the Atacama Desert, Chile: Implications for Mars

Here we inspect whether microbial life may disperse using dust transported by wind in the Atacama Desert in northern Chile, a well-known Mars analog model. By setting a simple experiment across the hyperarid core of the Atacama we found that a number of viable bacteria and fungi are in fact able to traverse the driest and most UV irradiated desert on Earth unscathed using wind-transported dust, particularly in the later afternoon hours. This finding suggests that microbial life on Mars, extant or past, may have similarly benefited from aeolian transport to move across the planet and find suitable habitats to thrive and evolve.

Colonization of the tsetse fly midgut with commensal Kosakonia cowanii Zambiae inhibits trypanosome infection establishment

Tsetse flies (Glossina spp.) vector pathogenic trypanosomes (Trypanosoma spp.) in sub-Saharan Africa. These parasites cause human and animal African trypanosomiases, which are debilitating diseases that inflict an enormous socio-economic burden on inhabitants of endemic regions. Current disease control strategies rely primarily on treating infected animals and reducing tsetse population densities. However, relevant programs are costly, labor intensive and difficult to sustain. As such, novel strategies aimed at reducing tsetse vector competence require development. Herein we investigated whether Kosakonia cowanii Zambiae (Kco_Z), which confers Anopheles gambiae with resistance to Plasmodium, is able to colonize tsetse and induce a trypanosome refractory phenotype in the fly. Kco_Z established stable infections in tsetse’s gut and exhibited no adverse effect on the fly’s survival. Flies with established Kco_Z infections in their gut were significantly more refractory to infection with two distinct trypanosome species (T. congolense, 6% infection; T. brucei, 32% infection) than were age-matched flies that did not house the exogenous bacterium (T. congolense, 36% infected; T. brucei, 70% infected). Additionally, 52% of Kco_Z colonized tsetse survived infection with entomopathogenic Serratia marcescens, compared with only 9% of their wild-type counterparts. These parasite and pathogen refractory phenotypes result from the fact that Kco_Z acidifies tsetse’s midgut environment, which inhibits trypanosome and Serratia growth and thus infection establishment. Finally, we determined that Kco_Z infection does not impact the fecundity of male or female tsetse, nor the ability of male flies to compete with their wild-type counterparts for mates. We propose that Kco_Z could be used as one component of an integrated strategy aimed at reducing the ability of tsetse to transmit pathogenic trypanosomes.

Tsetse flies transmit pathogenic African trypanosomes, which are the causative agents of socio-economically devastating human and animal African trypanosomiases. These diseases are currently controlled in large part by reducing the population size of tsetse vectors through the use of insecticides, traps and sterile insect technique. However, logistic and monetary hurdles often preclude the prolonged application of procedures necessary to maintain these control programs. Thus, novel strategies, including those aimed at sustainably reducing the ability of tsetse to transmit trypanosomes, are presently under development. Herein we stably colonize tsetse flies with a bacterium (Kosakonia cowanii Zambiae, Kco_Z) that acidifies their midgut, thus rendering the environment inhospitable to infection with two distinct, epidemiologically important trypanosome strains as well as an entomopathogenic bacteria. In addition to inducing a trypanosome refractory phenotype, colonization of tsetse with Kco_Z exerts only a modest fitness cost on the fly. Taken together, these findings suggest that Kco_Z could be applied to enhance the effectiveness of currently employed tsetse control programs.