Time-resolved analysis of a denitrifying bacterial community revealed a core microbiome responsible for the anaerobic degradation of quinoline

The biotechnological potential of the Chloroflexota phylum

In the next decades, the increasing material and energetic demand to support population growth and higher standards of living will amplify the current pressures on ecosystems and will call for greater investments in infrastructures and modern technologies. A valid approach to overcome such future challenges is the employment of sustainable bio-based technologies that explore the metabolic richness of microorganisms. Collectively, the metabolic capabilities of Chloroflexota, spanning aerobic and anaerobic conditions, thermophilic adaptability, anoxygenic photosynthesis, and utilization of toxic compounds as electron acceptors, underscore the phylum's resilience and ecological significance. These diverse metabolic strategies, driven by the interplay between temperature, oxygen availability, and energy metabolism, exemplify the complex adaptations that enabled Chloroflexota to colonize a wide range of ecological niches. In demonstrating the metabolic richness of the Chloroflexota phylum, specific members exemplify the diverse capabilities of these microorganisms: Chloroflexus aurantiacus showcases adaptability through its thermophilic and phototrophic growth, whereas members of the Anaerolineae class are known for their role in the degradation of complex organic compounds, contributing significantly to the carbon cycle in anaerobic environments, highlighting the phylum's potential for biotechnological exploitation in varying environmental conditions. In this context, the metabolic diversity of Chloroflexota must be considered a promising asset for a large range of applications. Currently, this bacterial phylum is organized into eight classes possessing different metabolic strategies to survive and thrive in a wide variety of extreme environments. This review correlates the ecological role of Chloroflexota in such environments with the potential application of their metabolisms in biotechnological approaches.

Nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the wild rice Oryza rufipogon core rhizomicrobiome

BACKGROUND

The assembly of the rhizomicrobiome, i.e., the microbiome in the soil adhering to the root, is influenced by soil conditions. Here, we investigated the core rhizomicrobiome of a wild plant species transplanted to an identical soil type with small differences in chemical factors and the impact of these soil chemistry differences on the core microbiome after long-term cultivation. We sampled three natural reserve populations of wild rice (i.e., in situ) and three populations of transplanted in situ wild rice grown ex situ for more than 40 years to determine the core wild rice rhizomicrobiome.

RESULTS

Generalized joint attribute modeling (GJAM) identified a total of 44 amplicon sequence variants (ASVs) composing the core wild rice rhizomicrobiome, including 35 bacterial ASVs belonging to the phyla Actinobacteria, Chloroflexi, Firmicutes, and Nitrospirae and 9 fungal ASVs belonging to the phyla Ascomycota, Basidiomycota, and Rozellomycota. Nine core bacterial ASVs belonging to the genera Haliangium, Anaeromyxobacter, Bradyrhizobium, and Bacillus were more abundant in the rhizosphere of ex situ wild rice than in the rhizosphere of in situ wild rice. The main ecological functions of the core microbiome were nitrogen fixation, manganese oxidation, aerobic chemoheterotrophy, chemoheterotrophy, and iron respiration, suggesting roles of the core rhizomicrobiome in improving nutrient resource acquisition for rice growth. The function of the core rhizosphere bacterial community was significantly (p < 0.05) shaped by electrical conductivity, total nitrogen, and available phosphorus present in the soil adhering to the roots.

CONCLUSION

We discovered that nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the core rhizomicrobiome of the wild rice Oryza rufipogon. Our findings suggest that further potential utilization of the core rhizomicrobiome should consider the effects of soil properties on the abundances of different genera. Video Abstract.

Biotechnological basis of microbial consortia for the removal of pesticides from the environment

The application of microbial strains as axenic cultures has frequently been employed in a diverse range of sectors. In the natural environment, microbes exist as multispecies and perform better than monocultures. Cell signaling and communication pathways play a key role in engineering microbial consortia, because in a consortium, the microorganisms communicate via diffusible signal molecules. Mixed microbial cultures have gained little attention due to the lack of proper knowledge about their interactions with each other. Some ideas have been proposed to deal with and study various microbes when they live together as a community, for biotechnological application purposes. In natural environments, microbes can possess unique metabolic features. Therefore, microbial consortia divide the metabolic burden among strains in the group and robustly perform pesticide degradation. Synthetic microbial consortia can perform the desired functions at naturally contaminated sites. Therefore, in this article, special attention is paid to the microbial consortia and their function in the natural environment. This review comprehensively discusses the recent applications of microbial consortia in pesticide degradation and environmental bioremediation. Moreover, the future directions of synthetic consortia have been explored. The review also explores the future perspectives and new platforms for these approaches, besides highlighting the practical understanding of the scientific information behind consortia.

Alkylphenols and Chlorophenols Remediation in Vertical Flow Constructed Wetlands: Removal Efficiency and Microbial Community Response

This study aims to investigate the effect of two different groups of phenolic compounds (the alkylphenols nonylphenol (NP) and octylphenol (OP), and the chlorophenol pentachlorophenol (PCP)) on constructed wetlands (CWs) performance, including on organic matter, nutrients and contaminants removal efficiency, and on microbial community structure in the plant bed substrate. CWs were assembled at lab scale simulating a vertical flow configuration and irrigated along eight weeks with Ribeira de Joane (an urban stream) water not doped (control) or doped with a mixture of NP and OP or with PCP (at a 100 μg·L−1 concentration each). The presence of the phenolic contaminants did not interfere in the removal of organic matter or nutrients in CWs in the long term. Removals of NP and OP were >99%, whereas PCP removals varied between 87% and 98%, mainly due to biodegradation. Microbial richness, diversity and dominance in CWs substrate were generally not affected by phenolic compounds, with only PCP decreasing diversity. Microbial community structure, however, showed that there was an adaptation of the microbial community to the presence of each contaminant, with several specialist genera being enriched following exposure. The three more abundant specialist genera were Methylotenera and Methylophilus (methylophilaceae family) and Hyphomicrobium (hyphomicrobiaceae family) when the systems were exposed to a mixture of NP and OP. When exposed to PCP, the three more abundant genera were Denitromonas (Rhodocyclaceae family), Xenococcus_PCC_7305 (Xenococcaceae family) and Rhodocyclaceae_uncultured (Rhodocyclaceae family). To increase CWs efficiency in the elimination of phenolic compounds, namely PCP which was not totally removed, strategies to stimulate (namely biostimulation) or increase (namely bioaugmentation) the presence of these bacteria should be explore. This study clearly shows the potential of vertical flow CWs for the removal of phenolic compounds, a still little explored subject, contributing to promote the use of CWs as nature-based solutions to remediate water contaminated with different families of persistent and/or emergent contaminants.

Guild-based analysis for understanding gut microbiome in human health and diseases

To demonstrate the causative role of gut microbiome in human health and diseases, we first need to identify, via next-generation sequencing, potentially important functional members associated with specific health outcomes and disease phenotypes. However, due to the strain-level genetic complexity of the gut microbiota, microbiome datasets are highly dimensional and highly sparse in nature, making it challenging to identify putative causative agents of a particular disease phenotype. Members of an ecosystem seldomly live independently from each other. Instead, they develop local interactions and form inter-member organizations to influence the ecosystem's higher-level patterns and functions. In the ecological study of macro-organisms, members are defined as belonging to the same "guild" if they exploit the same class of resources in a similar way or work together as a coherent functional group. Translating the concept of "guild" to the study of gut microbiota, we redefine guild as a group of bacteria that show consistent co-abundant behavior and likely to work together to contribute to the same ecological function. In this opinion article, we discuss how to use guilds as the aggregation unit to reduce dimensionality and sparsity in microbiome-wide association studies for identifying candidate gut bacteria that may causatively contribute to human health and diseases.

Bioelectrical Methane Production with an Ammonium Oxidative Reaction under the No Organic Substance Condition

The present study investigated bioelectrical methane production from CO₂ without organic substances. Even though microbial methane production has been reported at relatively high electric voltages, the amount of voltage required and the organisms contributing to the process currently remain unknown. Methane production using a biocathode was investigated in a microbial electrolysis cell coupled with an NH₄⁺ oxidative reaction at an anode coated with platinum powder under a wide range of applied voltages and anaerobic conditions. A microbial community analysis revealed that methane production simultaneously occurred with biological denitrification at the biocathode. During denitrification, NO₃^– was produced by chemical NH₄⁺ oxidation at the anode and was provided to the biocathode chamber. H₂ was produced at the biocathode by the hydrogen-producing bacteria Petrimonas through the acceptance of electrons and protons. The H₂ produced was biologically consumed by hydrogenotrophic methanogens of Methanobacterium and Methanobrevibacter with CO₂ uptake and by hydrogenotrophic denitrifiers of Azonexus. This microbial community suggests that methane is indirectly produced without the use of electrons by methanogens. Furthermore, bioelectrical methane production occurred under experimental conditions even at a very low voltage of 0.05‍ ‍V coupled with NH₄⁺ oxidation, which was thermodynamically feasible.

Multi-omic Directed Discovery of Cellulosomes, Polysaccharide Utilization Loci, and Lignocellulases from an Enriched Rumen Anaerobic Consortium

The lignocellulolytic ERAC displays a unique set of plant polysaccharide-degrading enzymes (with multimodular characteristics), cellulosomal complexes, and PULs. The MAGs described here represent an expansion of the genetic content of rumen bacterial genomes dedicated to plant polysaccharide degradation, therefore providing a valuable resource for the development of biocatalytic toolbox strategies to be applied to lignocellulose-based biorefineries.

Lignocellulose is one of the most abundant renewable carbon sources, representing an alternative to petroleum for the production of fuel and chemicals. Nonetheless, the lignocellulose saccharification process, to release sugars for downstream applications, is one of the most crucial factors economically challenging to its use. The synergism required among the various carbohydrate-active enzymes (CAZymes) for efficient lignocellulose breakdown is often not satisfactorily achieved with an enzyme mixture from a single strain. To overcome this challenge, enrichment strategies can be applied to develop microbial communities with an efficient CAZyme arsenal, incorporating complementary and synergistic properties, to improve lignocellulose deconstruction. We report a comprehensive and deep analysis of an enriched rumen anaerobic consortium (ERAC) established on sugarcane bagasse (SB). The lignocellulolytic abilities of the ERAC were confirmed by analyzing the depolymerization of bagasse by scanning electron microscopy, enzymatic assays, and mass spectrometry. Taxonomic analysis based on 16S rRNA sequencing elucidated the community enrichment process, which was marked by a higher abundance of Firmicutes and Synergistetes species. Shotgun metagenomic sequencing of the ERAC disclosed 41 metagenome-assembled genomes (MAGs) harboring cellulosomes and polysaccharide utilization loci (PULs), along with a high diversity of CAZymes. The amino acid sequences of the majority of the predicted CAZymes (60% of the total) shared less than 90% identity with the sequences found in public databases. Additionally, a clostridial MAG identified in this study produced proteins during consortium development with scaffoldin domains and CAZymes appended to dockerin modules, thus representing a novel cellulosome-producing microorganism.

IMPORTANCE The lignocellulolytic ERAC displays a unique set of plant polysaccharide-degrading enzymes (with multimodular characteristics), cellulosomal complexes, and PULs. The MAGs described here represent an expansion of the genetic content of rumen bacterial genomes dedicated to plant polysaccharide degradation, therefore providing a valuable resource for the development of biocatalytic toolbox strategies to be applied to lignocellulose-based biorefineries.

Antibiotic-induced role interchange between rare and predominant bacteria retained the function of a bacterial community for denitrifying quinoline degradation

AIM

Quinoline is a recalcitrant pollutant in coking wastewater which has been broadly investigated with many isolates possessing aerobic quinoline-degrading ability. However, studies on anaerobic degradation and the corresponding bacteria are very scarce. This study attempted to investigate the role of diverse functional members and the redundancy of quinoline degradation in a lab-scale quinoline denitrifying bioreactor.

METHODS AND RESULTS

Antibiotics were added to the batch culture under denitrifying conditions to disturb the microbial community of the quinoline-degrading bioreactor. According to the results, the nitrate removal rate remained stable, and the quinoline removal rate increased by 9·7% after treatment with streptomycin. However, PCoA analysis of 16S rRNA gene sequencing data of these samples indicated a significant shift in microbial community structures. Specifically, 12 operational taxonomic units (OTUs), including OTU1 (Pseudomonas) and OTU2 (Achromobacter), were significantly enriched. OTU1 replaced OTU8 (Thauera) as the most predominant denitrifying quinoline-degrading member. However, OTU8 and other predominant OTUs (Comamonas and Pseudoxanthomonas), which were hypothesized to contribute essentially to quinoline degradation in the origin bioreactor, became almost undetectable.

CONCLUSION

Functional redundancy due to high biological diversity allowed the role reversal of predominant quinoline-degrading bacteria and other rare bacteria when disturbed by antibiotic stress. Although the abundance of OTU1 was much lower initially, it replaced the essential role of the predominant member OTU8 in the bioreactor community for quinoline degradation once the environmental condition changed.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study indicated that the high biological diversity in a wastewater treatment bacterial community is crucial for maintaining the degrading function of organic pollutants, especially in a changing environment due to external disturbance or stress.

Cross-Feeding between Members of Thauera spp. and Rhodococcus spp. Drives Quinoline-Denitrifying Degradation in a Hypoxic Bioreactor

We experimentally verified that the second most abundant taxon, Rhodococcus, played a role in degrading quinoline to 2-hydroxyquinoline, while the most abundant taxon, Thauera, degraded 2-hydroxyquinoline. Metabolites from Thauera further served to provide metabolites for Rhodococcus. Hence, an ecological guild composed of two isolates was assembled, revealing the different roles that keystone organisms play in the microbial community. This report, to the best of our knowledge, is the first on cross-feeding between the initial quinoline degrader and a second bacterium. Specifically, the quinoline degrader (Rhodococcus) did not benefit metabolically from quinoline degradation to 2-hydroxyquinoline but instead benefited from the metabolites produced by the second bacterium (Thauera) when Thauera degraded the 2-hydroxyquinoline. These results could be a significant step forward in the elucidation of the microbial mechanism underlying quinoline-denitrifying degradation.

The complex bacterial community in a quinoline-degrading denitrifying bioreactor is predominated by several taxa, such as Thauera and Rhodococcus. However, it remains unclear how the interactions between the different bacteria mediate quinoline metabolism under denitrifying conditions. In this study, we designed a sequence-specific amplification strategy to isolate the most predominant bacteria and obtained four strains of Thauera aminoaromatica, a representative of a key member in the bioreactor. Tests on these isolates demonstrated that all were unable to degrade quinoline but efficiently degraded 2-hydroxyquinoline, the hypothesized primary intermediate of quinoline catabolism, under nitrate-reducing conditions. However, another isolate, Rhodococcus sp. YF3, corresponding to the second most abundant taxon in the same bioreactor, was found to degrade quinoline via 2-hydroxyquinoline. The end products and removal rate of quinoline by isolate YF3 largely varied according to the quantity of available oxygen. Specifically, quinoline could be converted only to 2-hydroxyquinoline without further transformation under insufficient oxygen conditions, e.g., less than 0.5% initial oxygen in the vials. However, resting YF3 cells aerobically precultured in medium with quinoline could anaerobically convert quinoline to 2-hydroxyquinoline. A two-strain consortium constructed with isolates from Thauera (R2) and Rhodococcus (YF3) demonstrated efficient denitrifying degradation of quinoline. Thus, we experimentally verified that the metabolic interaction based on 2-hydroxyquinoline cross-feeding between two predominant bacteria constitutes the main quinoline degradation mechanism. This work uncovers the mechanism of quinoline removal by two cooperative bacterial species existing in denitrifying bioreactors.

IMPORTANCE We experimentally verified that the second most abundant taxon, Rhodococcus, played a role in degrading quinoline to 2-hydroxyquinoline, while the most abundant taxon, Thauera, degraded 2-hydroxyquinoline. Metabolites from Thauera further served to provide metabolites for Rhodococcus. Hence, an ecological guild composed of two isolates was assembled, revealing the different roles that keystone organisms play in the microbial community. This report, to the best of our knowledge, is the first on cross-feeding between the initial quinoline degrader and a second bacterium. Specifically, the quinoline degrader (Rhodococcus) did not benefit metabolically from quinoline degradation to 2-hydroxyquinoline but instead benefited from the metabolites produced by the second bacterium (Thauera) when Thauera degraded the 2-hydroxyquinoline. These results could be a significant step forward in the elucidation of the microbial mechanism underlying quinoline-denitrifying degradation.

Endophyte-assisted phytoremediation: mechanisms and current application strategies for soil mixed pollutants

Phytoremediation uses plants and associated microbes to remove pollutants from the environment and is considered a promising bioremediation method. Compared with well-described single contaminant treatments, the number of studies reporting phytoremediation of soil mixed pollutants has increased recently. Endophytes, including bacteria and fungi, exhibit beneficial traits for the promotion of plant growth, stress alleviation, and biodegradation. Moreover, endophytes either directly or indirectly assist host plants to survive high concentrations of organic and inorganic pollutants in the soil. Endophytic microorganisms can also regulate the plant metabolism in different ways, exhibiting a variety of physiological characteristics. This review summarizes the taxa and physiological properties of endophytic microorganisms that may participate in the detoxification of contaminant mixtures. Furthermore, potential biomolecules that may enhance endophyte mediated phytoremediation are discussed. The practical applications of pollutant-degrading endophytes and current strategies for applying this valuable bio-resource to soil phytoremediation are summarized.

Enhanced quinoline removal by zero-valent iron-coupled novel anaerobic processes: performance and underlying function analysis

Quinoline is toxic and difficult to degrade biologically; thus, it is a serious threat to the safety of ecosystems. To promote quinoline reduction, zero-valent iron (ZVI) was introduced into an anaerobic digestion (AD) system through batch experiments. The performance of three different types of ZVI (i.e., iron powder, iron scrap and rusty iron scrap) on quinoline degradation, methane production, formation of volatile fatty acids (VFAs) and chemical oxygen demand (COD) removal were investigated systematically. Compared to the AD system alone, quinoline and COD removal as well as the production of methane and acetic acid were effectively enhanced by ZVI, especially rusty iron scrap. The removal efficiencies of quinoline and COD were increased by 28.6% and 19.9%, respectively. The enhanced effects were attributed to the high accumulation of ferrous ions and high pH self-buffering capability, which were established by ZVI addition. Furthermore, high-throughput sequencing analysis indicated that the functional microorganisms in the ZVI-AD system were higher than in the AD system, and the added types of ZVI played important roles in structuring the innate microbial community in waste activated sludge (WAS). Especially, high enrichment of microorganisms capable of degrading quinoline, such as Pseudomonas and Bacillus, in the coupled system was detected.

The Advanced Anaerobic Expanded Granular Sludge Bed (AnaEG) Possessed Temporally and Spatially Stable Treatment Performance and Microbial Community in Treating Starch Processing Wastewater

This study implements temporal and spatial appraisals on the operational performance and corresponding microbial community structure of a full-scale advanced anaerobic expanded granular sludge bed (AnaEG) which was used to treat low organic loading starch processing wastewater. Results showed stable treatment efficiency could be maintained with long-term erratic influent quality, and a major reaction zone located at the bottom of the AnaEG, where the main pollutant removal rate was greater than 90%. Remarkably, high-throughput sequencing of 16S rRNA gene amplicons displayed that the predominant members constructed the major part of the overall microbial community and showed highly temporal stability. They were affiliated to Chloroflexi (16.4%), Proteobacteria (14.01%), Firmicutes (8.76%), Bacteroidetes (7.85%), Cloacimonetes (3.21%), Ignavibacteriae (1.80%), Synergistetes (1.11%), Thermotogae (0.98%), and Euryarchaeota (3.18%). This part of microorganism implemented the long-term stable treatment efficiency of the reactor. Simultaneously, an extraordinary spatial homogeneity in the granule physic properties and microbial community structure along the vertical direction was observed within the AnaEG. In conclusion, the microbial community structure and the bioreactor’s performance showed notable spatial and temporal consistency, and the predominant populations guaranteed a long-term favorable treatment performance of the AnaEG. It provides us with a better understanding of the mechanism of this recently proposed anaerobic reactor which was used in low organic loading wastewater treatment.

Degradation shaped bacterial and archaeal communities with predictable taxa and their association patterns in Zoige wetland at Tibet plateau

Soil microbes provide important ecosystem services. Zoige Plateau wetland, the largest alpine peat wetland in the world, has suffered from serious degradation in the past 30 years. We studied the composition of the Zoige Plateau alpine wetland soil microbiota and relations among specific taxa using 16S rRNA amplicon sequencing combined with association network analysis. Compared to the pristine swamp soil, taxons DA101, Aeromicrobium, Bradyrhizobium, and Candidatus Nitrososphaera were enriched and several methanogenic Euryarchaeota were depleted in the moderately degraded meadow soil and highly degraded sandy soil. Soil total potassium contents in soils with different degradation levels were significantly different, being the highest in meadow soil and lowest in swamp soil. The association network analysis showed that total potassium positively correlated with specific bacterial and archaeal taxa. Jiangella, Anaerolinea, Desulfobulbus, Geobacter, Flavobacterium, Methanobacterium and Methanosaeta were identified as the keystone genera in the networks. Soil degradation affected soil properties, and caused changes in the bacterial and archaeal community composition and the association patterns of community members. The changes could serve as early warning signals of soil degradation in alpine wetlands.