Diversity of microbiota found in coffee processing wastewater treatment plant

Impact of lead (Pb2+) on the growth and biological activity of Serratia marcescens selected for wastewater treatment and identification of its zntR gene-a metal efflux regulator

Microorganisms isolated from contaminated areas play an important role in bioremediation processes. They promote heavy metal removal from the environment by adsorbing ions onto the cell wall surface, accumulating them inside the cells, or reducing, complexing, or precipitating these substances in the environment. Microorganism-based bioremediation processes can be highly efficient, low-cost and have low environmental impact. Thus, the present study aimed to select Pb²⁺-resistant bacteria and evaluate the growth rate, biological activity, and the presence of genes associated with metal resistance. Serratia marcescens CCMA 1010, that was previously isolated from coffee processing wastewater, was selected since was able to growth in Pb²⁺ concentrations of up to 4.0 mM. The growth rate and generation time did not differ from those of the control (without Pb²⁺), although biological activity decreased in the first hour of exposure to these ions and stabilized after this period. The presence of the zntR, zntA and pbrA genes was analysed, and only zntR was detected. The zntR gene encodes a protein responsible for regulating the production of ZntA, a transmembrane protein that facilitates Pb²⁺ extrusion out of the cell. S. marcescens CCMA 1010 demonstrated a potential for use as bioindicator that has potential to be used in bioremediation processes due to its resistance to high concentrations of Pb²⁺, ability to grow until 24 h of exposure, and possession of a gene that indicates the existence of mechanisms associated with resistance to lead (Pb²⁺).

Biotreatment Potential and Microbial Communities in Aerobic Bioreactor Systems Treating Agro-Industrial Wastewaters

The thriving agro-industry sector accounts for an essential part of the global gross domestic product, as the need for food and feed production is rising. However, the industrial processing of agricultural products requires the use of water at all stages, which consequently leads to the production of vast amounts of effluents with diverse characteristics, which contain a significantly elevated organic content. This fact reinforces the need for action to control and minimize the environmental impact of the produced wastewater, and activated sludge systems constitute a highly reliable solution for its treatment. The current review offers novel insights on the efficiency of aerobic biosystems in the treatment of agro-industrial wastewaters and their ecology, with an additional focus on the biotechnological potential of the activated sludge of such wastewater treatment plants.

An Updated Global Species Diversity and Phylogeny in the Genus Wickerhamomyces with Addition of Two New Species from Thailand

Ascomycetous yeast species in the genus Wickerhamomyces (Saccharomycetales, Wickerhamomycetaceae) are isolated from various habitats and distributed throughout the world. Prior to this study, 35 species had been validly published and accepted into this genus. Beneficially, Wickerhamomyces species have been used in a number of biotechnologically applications of environment, food, beverage industries, biofuel, medicine and agriculture. However, in some studies, Wickerhamomyces species have been identified as an opportunistic human pathogen. Through an overview of diversity, taxonomy and recently published literature, we have updated a brief review of Wickerhamomyces. Moreover, two new Wickerhamomyces species were isolated from the soil samples of Assam tea (Camellia sinensis var. assamica) that were collected from plantations in northern Thailand. Herein, we have identified these species as W. lannaensis and W. nanensis. The identification of these species was based on phenotypic (morphological, biochemical and physiological characteristics) and molecular analyses. Phylogenetic analyses of a combination of the internal transcribed spacer (ITS) region and the D1/D2 domains of the large subunit (LSU) of ribosomal DNA genes support that W. lannaensis and W. nanensis are distinct from other species within the genus Wickerhamomyces. A full description, illustrations and a phylogenetic tree showing the position of both new species have been provided. Accordingly, a new combination species, W. myanmarensis has been proposed based on the phylogenetic results. A new key for species identification is provided.

High-throughput 16S rRNA gene sequencing of the microbial community associated with palm oil mill effluents of two oil processing systems

Palm Oil Mill Effluents (POME) are complex fermentative substrates which habour diverse native microbial contaminants. However, knowledge on the microbiota community shift caused by the anthropogenic effects of POME in the environment is up to date still to be extensively documented. In this study, the bacterial and archaeal communities of POME from two palm oil processing systems (artisanal and industrial) were investigated by Illumina MiSeq Platform. Despite the common characteristics of these wastewaters, we found that their microbial communities were significantly different with regard to their diversity and relative abundance of their different Amplicon Sequence Variants (ASV). Indeed, POME from industrial plants harboured as dominant phyla Firmicutes (46.24%), Bacteroidetes (34.19%), Proteobacteria (15.11%), with the particular presence of Spirochaetes, verrucomicrobia and Synergistetes, while those from artisanal production were colonized by Firmicutes (92.06%), Proteobacteria (4.21%) and Actinobacteria (2.09%). Furthermore, 43 AVSs of archaea were detected only in POME from industrial plants and assigned to Crenarchaeota, Diapherotrites, Euryarchaeota and Nanoarchaeaeota phyla, populated mainly by many methane-forming archaea. Definitively, the microbial community composition of POME from both type of processing was markedly different, showing that the history of these ecosystems and various processing conditions have a great impact on each microbial community structure and diversity. By improving knowledge about this microbiome, the results also provide insight into the potential microbial contaminants of soils and rivers receiving these wastewaters.

Microbial diversity associated with spontaneous coffee bean fermentation process and specialty coffee production in northern Colombia

Coffee fermentation involves the action of microorganisms, whose metabolism has a significant influence on the composition of the beans and, consequently, on the beverage's sensory characteristics. In this study, the microbial diversity during the wet fermentation of Coffea arabica L. in the Sierra Nevada of Santa Marta (SNSM) in Colombia was explored by high-throughput sequencing and the resulting cup quality through the standards of the Specialty Coffee Association. The taxonomic assignment of sequence reads showed a high microbial diversity comprised of 695 bacterial and 156 fungal genera. The microbial community was dominated by the Lactic Acid Bacteria (LAB) Leuconostoc, the yeast Kazachstania, and the Acetic Acid Bacteria (AAB) Acetobacter. Co-occurrence relationships suggested synergistic patterns between populations of LAB-AAB, yeasts-AAB, Leuconostoc-Prevotella, LAB-ABB-Selenomonas, and yeasts-fungi-nonLAB-nonAAB, which may result in the production of metabolites that positively impact the sensory attributes of coffee. The beverages produced were classified as specialty coffees, and their score was positively influenced by the fungal richness and the abundance of unclassified Lactobacillales, Pichia, and Pseudomonas. The findings show the richness and microbial diversity of the SNSM and serve as input for future research such as the analysis of microbial-derived metabolites and the establishment of starter cultures in coffee processing that guarantee the generation of high-quality beverages, the standardization of processes, the reduction of economic losses, and the production of value-added products that allow taking advantage of specialty coffee market.

Tailoring Next Generation Plant Growth Promoting Microorganisms as Versatile Tools beyond Soil Desalinization: A Road Map towards Field Application

Plant growth promoting bacteria (PGPB) have been the target of intensive research studies toward their efficient use in the field as biofertilizers, biocontrol, and bioremediation agents among numerous other applications. Recent trends in the field of PGPB research led to the development of versatile multifaceted PGPB that can be used in different field conditions such as biocontrol of plant pathogens in metal contaminated soils. Unfortunately, all these research efforts lead to the development of PGPB that failed to perform in salty environments. Therefore, it is urgently needed to address this drawback of these PGPB toward their efficient performance in salinity context. In this paper we provide a review of state-of-the-art research in the field of PGPB and propose a road map for the development of next generation versatile and multifaceted PGPB that can perform in salinity. Beyond soil desalinization, our study paves the way towards the development of PGPB able to provide services in diverse salty environments such as heavy metal contaminated, or pathogen threatened. Smart development of salinity adapted next generation biofertilizers will inevitably allow for mitigation and alleviation of biotic and abiotic threats to plant productivity in salty environments.

Protocol to select efficient microorganisms to treat coffee wastewater

The coffee processing wastewater (CPWW) requires treatment before being disposed of in the environment or reused due to its high organic and inorganic composition and a low pH. The indigenous microbiota from CPWW is highly diverse and could be selected as inoculums in treatment waste plants. Considering the physico-chemical characteristics of wastewater coffee, we elaborate on steps to select the microbial consortium that showed positive impact via decreasing the pollutant parameters of this effluent. The effectiveness was confirmed using wastewater from different origins with different chemical characteristics. A bacterial consortium composed by Serratia marcescens CCMA 1010 and CCMA 1012, Corynebacterium flavescens CCMA 1006, and Acetobacter indonesiensis CCMA 1002 was selected as the inoculums-based phenotypic assays. The mixed inoculum showed a highly active population (11.18 log CFU mL^-1), promoting an 85% decrease in biochemical oxygen demand and a 60% decrease in chemical oxygen demand. There was also an 80% reduction in phosphorus and nitrogen. The final pH changed from 6.0 to 7.5. Additionally, the eco-toxicity using Daphnia similis was reduced by more than 59%. The microbial inoculum was efficient in the biological treatment in CPWWs, demonstrating the efficiency and robustness of the selected strains, independent of the physico-chemical characteristics of wastewater.

Coffee Microbiota and Its Potential Use in Sustainable Crop Management. A Review

Intensive coffee production is accompanied by several environmental issues, including soil degradation, biodiversity loss, and pollution due to the wide use of agrochemical inputs and wastes generated by processing. In addition, climate change is expected to decrease the suitability of cultivated areas while potentially increasing the distribution and impact of pests and diseases. In this context, the coffee microbiota has been increasingly studied over the past decades in order to improve the sustainability of the coffee production. Therefore, coffee associated microorganisms have been isolated and characterized in order to highlight their useful characteristics and study their potential use as sustainable alternatives to agrochemical inputs. Indeed, several microorganisms (including bacteria and fungi) are able to display plant growth-promoting capacities and/or biocontrol abilities toward coffee pests and diseases. Despite that numerous studies emphasized the potential of coffee-associated microorganisms under controlled environments, the present review highlights the lack of confirmation of such beneficial effects under field conditions. Nowadays, next-generation sequencing technologies allow to study coffee associated microorganisms with a metabarcoding/metagenomic approach. This strategy, which does not require cultivating microorganisms, now provides a deeper insight in the coffee-associated microbial communities and their implication not only in the coffee plant fitness but also in the quality of the final product. The present review aims at (i) providing an extensive description of coffee microbiota diversity both at the farming and processing levels, (ii) identifying the “coffee core microbiota,” (iii) making an overview of microbiota ability to promote coffee plant growth and to control its pests and diseases, and (iv) highlighting the microbiota potential to improve coffee quality and waste management sustainability.

Aquatic yeasts: diversity, characteristics and potential health implications

There has been a rising interest in the levels, diversity and potential impacts of yeasts in aquatic environments. Some of the species isolated from such niches are known pathogens or have pathogenic and antifungal resistance features. This deems it necessary to understand the characteristics and potential health implications of such environmental yeasts species. Studies on these subjects are limited. Most studies on aquatic yeasts have linked them to water pollution. However, the current gold standards to determine microbial pollution of water use bacteria as the main indicator organisms. Including yeasts in water quality standards may provide a different dimension on the quality of water when determining its fit-for-use properties. Pathogenic yeasts cause superficial infections or life-threatening infections, especially in immunocompromised people. Some of the yeast species isolated in recent studies were resistant to commonly used antifungal agents of clinical and veterinary relevance. With the high prevalence rate of HIV in sub-Saharan Africa, particularly in South Africa, antifungal resistance is a public concern as it poses serious medical and economic challenges. Most available studies are concerned with clinical environments only. There is, thus, a need to review the literature that also focuses on aquatic environments.

Assessing the efficiency in assisted depuration of coffee processing wastewater from mixed wild microbial selected inoculum

This work evaluated the efficiency of bacterial bio-augmentation to the biological treatment of coffee processing wastewater (CPWW) in a pilot wastewater treatment plant (WTP). Biochemical oxygen demand (BOD) and chemical oxygen demand (COD) values were the basis for the treatment efficiency. Serratia marcescens CCMA 1010 and CCMA 1013, Corynebacterium flavescens CCMA 1006 and Acetobacter indonesiensis CCMA 1002 were previously selected. The microbial cocktail was inoculated and persisted in CPWW during all treatments. The richness of wild species was a little altered over time and up to nine species were found in each sampled season. The microbiota composition presented variation of a total of 13 species, despite the inoculation of the microbial inoculum. The biodegradability index of effluent, close to 0.5, was favourable to biological treatment. The pollution parameters of CPWW were decreased in function of the variation of community composition and microbial activity. The greatest reduction of BOD (~ 33%) and COD (~ 25%) was observed between 72 h and 8 days of the biological treatment. The CPWW toxicity in Allium cepa seeds was lower by up to 60%, and the germination index (GI) exceeded 100% in the treated CPWW. The results of the CPWW biological treatment by bio-augmentation from native micro-organisms in the pilot-scale WTP indicated the greatest efficiency relating to the spontaneous biological treatment of CPWW. After this treatment, the discharge of effluent in the environment would not have toxic effects on the plants.

Biological nitrogen removal and metabolic characteristics of a novel aerobic denitrifying fungus Hanseniaspora uvarum strain KPL108

A novel aerobic denitrifying fungal strain KPL108 was isolated from the sediment of Jinpen drinking water reservoir and identified as Hanseniaspora uvarum. Strain KPL108 removed 99% of nitrate without nitrite accumulation under aerobic conditions, while the total organic carbon removal efficiency was 93%. KPL108 expressed fungal specific denitrifying gene p450nor. Nitrogen balance exhibited that approximately 92% of the initial nitrate was removed as gaseous products. Based on ¹³C-isotope labeling tracer, pentose phosphate pathway and tricarboxylic acid cycle were highly active in intracellular central carbon metabolism of strain KPL108. Response surface methodology revealed that the maximum total nitrogen removal efficiency occurred with the optimized parameters: C/N ratio of 6.4, pH of 8.2, 28.5 °C and 109.7 rpm. Collectively, the results from the present study indicate that strain KPL108 has aerobic denitrification ability, which has a great potential application for nitrogenous wastewater treatment.

Predominance of syntrophic bacteria, Methanosaeta and Methanoculleus in a two-stage up-flow anaerobic sludge blanket reactor treating coffee processing wastewater at high organic loading rate

The effect of the organic loading rate (OLR) on the performance and microbial composition of a two-stage UASB system treating coffee processing wastewater was assessed. The system was operated with OLR up to 18.2 g COD (L d)^-1 and effluent recirculation. Methane production and effluent characteristics were monitored. The microbial composition was examined through next-generation sequencing and qPCR from the anaerobic sludge of the first reactor (R1) operated at low and high OLR. The system showed operational stability, obtaining a maximum methane production of 2.2 L CH₄ (L d)^-1, with a removal efficiency of COD and phenolic compounds of 84 and 73%, respectively. The performance of R1 at high OLR in steady conditions was associated with an appropriate proportion of nutrients (particularly Fe) and a marked increase of the syntrophic bacteria Syntrophus and Candidatus Cloacimonas, and acetoclastic and hydrogenotrophic methanogens, mainly Methanosaeta, Methanoculleus, Methanobacterium and Methanomassiliicoccus.