Understanding microbiome dynamics and functional responses during acidogenic fermentation of sucrose and sugarcane vinasse through metatranscriptomic analysis

Improving anaerobic digestion of sugarcane vinasse - a high-strength wastewater from ethanol distillation - is a subject of great interest, in view of the reduction of the pollutants and recovery of methane and valuable metabolites as byproducts. Through metatranscriptomic analysis, this study evaluated the active microbiome and metabolic pathways in a continuous acidogenic reactor: Stage 1S (control): 100% sucrose-based substrate (SBS); Stage 2SV (acclimation): 50% SBS and 50% vinasse; Stage 3V: 100% vinasse. Metatranscriptome obtained from each Stage was subjected to taxonomic and functional annotations. Under SBS feeding, pH dropped to pH 2.7 and biohydrogen production was observed. As vinasse was added, pH increased to 4.1-4.5, resulting in community structure and metabolite changes. In Stage 3V, biohydrogen production ceased, and propionate and acetate prevailed among the volatile fatty acids. Release of homoacetogenesis enzymes by Clostridium ljungdahlii and of uptake hydrogenase (EC 1.12.99.6) by Pectinatus frisingensis were linked to hydrogen consumption in Stages 2SV and 3V. Metabolic pathways of vinasse compounds, such as carbohydrates, malate, oxalate, glycerol, sulfate and phenol, were investigated in detail. In pyruvate metabolism, gene transcripts of oadA (oxaloacetate decarboxylase) and mdh (malate dehydrogenase), were upregulated in Stage 3V, being mostly attributed to P. frisingensis. Acetate formation from vinasse degradation was mainly attributed to Megasphaera and Clostridium, and propionate formation to P. frisingensis. Glycerol removal from vinasse exceeded 99%, and gene transcripts encoding for glpF (glycerol uptake facilitator protein), glpK (glycerol kinase) and glpABC (glycerol-3-phosphate dehydrogenase) were expressed mostly by Pectinatus and Prevotella. mRNA profiling showed that active bacteria and gene expression greatly changed when vinasse replaced sucrose, and Pectinatus was the main active bacterium degrading the searched compounds from vinasse. The identification of the main metabolic routes and the associated microorganisms achieved in this work contributes with valuable information to support further optimization of fermentation towards the desired metabolites.

Extremophilic taxa predominate in a microbial community of photovoltaic panels in a tropical region

Photovoltaic panels can be colonized by a highly diverse microbial diversity, despite life-threatening conditions. Although they are distributed worldwide, the microorganisms living on their surfaces have never been profiled in tropical regions using 16S rRNA high-throughput sequencing and PICRUst metagenome prediction of functional content. In this work, we investigated photovoltaic panels from two cities in southeast Brazil, Sorocaba and Itatiba, using these bioinformatics approach. Results showed that, despite significant differences in microbial diversity (p < 0.001), the taxonomic profile was very similar for both photovoltaic panels, dominated mainly by Proteobacteria, Bacteroidota and lower amounts of Cyanobacteria phyla. A predominance of Hymenobacter and Methylobacterium-Methylorubrum was observed at the genus level. We identified a microbial common core composed of Hymenobacter, Deinococcus, Sphingomonas, Methylobacterium-Methylorubrum, Craurococcus-Caldovatus, Massilia, Noviherbaspirillum and 1174-901-12 sharing genera. Predicted metabolisms focused on specific genes associated to radiation and desiccation resistance and pigments, were detected in members of the common core and among the most abundant genera. Our results suggested that taxonomic and functional profiles investigated were consistent with the harsh environment that photovoltaic panels represent. Moreover, the presence of stress genes in the predicted functional content was a preliminary evidence that microbes living there are a possibly source of metabolites with biotechnological interest.

In-depth assessment of microbial communities in the full-scale vertical flow treatment wetlands fed with raw domestic wastewater

A multiphase study was proposed to examine microbial communities linked to the nitrogen cycle in the first stage of four full-scale French vertical flow treatment systems. To this end, denaturing gradient gel electrophoresis (DGGE) was performed for structural assessment and quantitative PCR (qPCR) to enumerate the abundance of ammonia-oxidizing (AOB). 16S rRNA sequencing was used to assess the taxonomic profile followed by putative assessment of functional genes. The samples were collected under different conditions, such as operational time (presence/absence of sludge layer on the surface of the filters), season (winter and summer), sampling depth (0, 15 and 30 cm) and operation cycle (rest and feed periods). A structural disparity was noted in the upper layers, whereas higher similarity at 30 cm was observed highlighting the effect of organic matter on bacterial diversity. The 7th rest day was highlighted by an apparent decline in the microbial community abundance. Additionally, qPCR indicated that the largest amount of AOB was found at 30 cm depth and during the feeding period. From the taxonomic profile, Mycobacterium, Acinetobacter, Flavobacterium, and Nitrospira were the most abundant genre found in all systems. The functional prediction results showed predicted genes linked to the denitrification process. The results suggested that operating time and season were responsible for the pattern of the microbial community behavior. This study allowed us to further understand the bacterial dynamics and to advance the idea of design modifications made in the first stage of the classical French system to improve nitrogen removal are promising.

Microbiome taxonomic and functional profiles of two domestic sewage treatment systems

Anaerobic systems for domestic sewage treatment, like septic tanks and anaerobic filters, are used in developing countries due to favorable economic and functional features. The anaerobic filter is used for the treatment of the septic tank effluent, to improve the COD removal efficiency of the system. The microbial composition and diversity of the microbiome from two wastewater treatment systems (factory and rural school) were compared through 16S rRNA gene sequencing using MiSeq 2 × 250 bp Illumina sequencing platform. Additionally, 16S rRNA data were used to predict the functional profile of the microbial communities using PICRUSt2. Results indicated that hydrogenotrophic methanogens, like Methanobacterium, were found in higher abundance in both systems compared to acetotrophic methanogens belonging to Methanosaeta genus. Also, important syntrophic microorganisms (Smithella, Syntrophus, Syntrophobacter) were found in the factory and rural school wastewater treatment systems. Microbial communities were also compared between stages (septic tank and anaerobic filter) of each wastewater treatment stage, revealing that, in the case of the rural school, both microbial communities were quite similar most likely due to hydraulic short-circuit issues. Meanwhile, in the factory, microbial communities from the septic tank and anaerobic filter were different. The school system showed lower COD removal rates (2-30%), which were probably related to a higher abundance of Firmicutes members in addition to the hydraulic short-circuit and low abundance of Chloroflexi members. On the other hand, the fiberglass factory presented higher COD removal rates (60-83%), harboring phyla reported as the core microbiome of anaerobic digesters (Bacteroidetes, Chloroflexi, and Proteobacteria phyla). The knowledge of the structure and composition of wastewater treatment systems may provide support for the improvement of the pollutant removal in anaerobic process.

Microaerated UASB reactor treating textile wastewater: The core microbiome and removal of azo dye Direct Black 22

Sequential anaerobic and aerobic processes have been recommended to treat textile wastewater reliably. In this work, the focus was on finding an energetically more competitive system to remove tetra-azo dye Direct Black 22 (DB22). We operated two upflow anaerobic sludge blanket (UASB) reactors (R1 and R2) in three phases (PI, PII, and PIII). R1 was operated as a conventional UASB, while R2 was microaerated in the upper part (0.18 ± 0.05 mg O₂. L^-1), aiming to remove DB22 simultaneously with the aromatic amine byproducts. PI consisted of feeding reactors with synthetic textile wastewater (STW), PII had higher salinity in the STW, and PIII was the same as PII, plus sulfate. The results showed that color and COD removal efficiencies were similar for both reactors (67-72% for R1 and 59-78% for R2) without a substantial influence of oxygen in R2. However, microaeration played a crucial role in R2 by removing the anaerobically formed aromatic amines; during PIII, the effluent was 16 times less toxic than that of R1. The microbial community that developed in the sludge bed of both reactors was quite similar, with the core microbiome represented by Trichococcus, Syntrophus and Methanosaeta genera. The increase in salinity in PII and PIII promoted a shift in the microbial community, excluding salty-sensitive genera from the core microbiome. The putative genera Brevundimonas and Ornatilinea were associated to aromatic amine microaerobic removal. Therefore, there is a potential application of a compact microaerated anaerobic system for textile wastewater treatment.

Unveiling resistome profiles in the sediments of an Antarctic volcanic island

The Deception Island, located in Maritime Antarctica, is a volcanic island with geothermal activity and one of the most visited by tourists. However, the extent of the anthropogenic impact remains largely unknown and the factors shaping the resistance/tolerance mechanisms in the microbiomes from Whalers Bay ecosystems have never been investigated. In this context, this study aimed to reveal the resistome profiles of Whalers Bay sediments and correlate them with environmental factors. Samples were collected at four sites during the summer 2014/2015 along a transect of 27.5 m in the Whalers Bay sediments. DNA isolated from sediment samples was sequenced using the Illumina HiSeq platform. Bioinformatic analyses allowed the assembly of contigs and scaffolds, prediction of ORFs, and taxonomic and functional annotation using NCBI RefSeq database and KEGG orthology, respectively. Microorganisms belonging to the genera Psychrobacter, Flavobacterium and Polaromonas were shown to dominate all sites, representing 60% of taxonomic annotation. Arsenic (As), copper (Cu) and iron (Fe) were the most abundant metal resistance/tolerance types found in the microbiomes. Beta-lactam was the most common class related to antibiotics resistance/tolerance, corroborating with previous environmental resistome studies. The acridine class was the most abundant amongst the biocide resistance/tolerances, related to antiseptic compounds. Results gathered in this study reveal a repertoire of resistance/tolerance classes to antibiotics and biocides unusually found in Antarctica. However, given the volcanic nature (heavy metals-rich region) of Deception Island soils, this putative impact must be viewed with caution.

Laundry wastewater and domestic sewage pilot-scale anaerobic treatment: Microbial community resilience regarding sulfide production

In this study, the removal of anionic surfactant Linear Alkylbenzene Sulfonate (LAS) from laundry wastewater was evaluated in co-digestion with domestic sewage, using a pilot-scale Expanded Granular Sludge Bed reactor. Surfactant influent concentration was enhanced from 5 ± 3 mg LAS L^-1 (stage I) to 19 ± 10 mg LAS L^-1 (stage II) and 36 ± 19 mg LAS L^-1 (stage III) throughout reactor operation. Sulfide levels higher than 20 mg L^-1 influenced LAS removal efficiency, which decreased from 71% to 55% and 32% in stage I, II and III, respectively. Acclimation of microbial population was verified and higher relative abundance of the genera similar to Cytophaga, Bacteroides, Syntrophus and Syntrophobacter in the early stages (adaptation and stage I) was replaced by higher relative abundance of the genera Anaerophaga, Nitrosovibrio, Sulfurovum and Desulfovibrio in the last stages (stage II and III).

Land Use and Seasonal Effects on the Soil Microbiome of a Brazilian Dry Forest

Drylands occupy approximately 41% of the Earth's terrestrial surface. Climate change and land use practices are expected to affect biogeochemical cycling by the soil microbiome in these ecosystems. Understanding how soil microbial community might respond to these drivers is extremely important to mitigate the processes of land degradation and desertification. The Caatinga, an exclusively Brazilian biome composed of an extensive seasonal tropical dry forest, is exposed to variable spatiotemporal rainfall patterns as well as strong human-driven pressures. Herein, an integrated analysis of shotgun metagenomics approach coupled to meteorological data was employed to unravel the impact of seasonality and land use change on soil microbiome from preserved and agriculture-affected experimental fields in Caatinga drylands. Multivariate analysis suggested that microbial communities of preserved soils under seasonal changes were shaped primarily by water deficit, with a strong increase of Actinobacteria and Proteobacteria members in the dry and rainy seasons, respectively. In contrast, nutrient availability notably played a critical role in driving the microbial community in agriculture-affected soils. The strong enrichment of bacterial genera belonging to the poorly-known phylum Acidobacteria ('Candidatus Solibacter' and 'Candidatus Koribacter') in soils from dry season affected by ferti-irrigation practices presupposes a contrasting copiotrophic lifestyle and ecological role in mitigating the impact of chemical fertilization. Functional analyses identify overrepresented genes related to osmotic stress response (synthesis of osmoprotectant compounds, accumulation of potassium ions) and preferential carbon and nitrogen utilization when comparing the microbiome of preserved soils under seasonal changes, reflecting differences in the genetic potential for nutrient cycling and C acquisition in the environment. However, the prevalence of nitrosative stress and denitrification functions in irrigation/fertilization-affected soils of the dry season clearly suggest that nutrient input and disruption of natural water regime may impact biogeochemical cycles linked to the microbial processes, with potential impacts on the ecosystem functionality. These findings help to better understand how natural seasonality and agricultural management differentially affect soil microbial ecology from dry forests, providing support for the development of more sustainable land management in dryland ecosystems.

Comparative metatranscriptomic analysis of anaerobic digesters treating anionic surfactant contaminated wastewater

Three distinct biological reactors fed with synthetic medium (UASB_Control), synthetic medium and linear alkylbenzene sulfonate (LAS; UASB_SL), and real laundry wastewater (UASB_LW) were compared using a metatranscriptomic approach to determine putative bioindicator genes and taxonomies associated to all steps of anaerobic LAS biodegradation pathway. A homemade bioinformatics pipeline combined with an R workflow was developed to perform the RNAseq data analysis. UASB_SL and UASB_LW showed similar values of LAS biological degradation (~47%) and removal (53-55%). Rarefaction analysis revealed that 1-2 million reads were sufficient to access the whole functional capacity. In the first step of LAS biodegradation pathway, fumarate reductase subunit C was detected and taxonomically assigned to the genus Syntrophobacter (0.002% - UASB_SL; 0.0015% - UASB_LW; not detected - UASB_Control). In the second step, many enzymes related to beta-oxidation were observed and most of them with low relative abundance in UASB Control and taxonomically related with Smithella, Acinetobacter and Syntrophorhabdus. For the ring cleavage step, the abundance of 6 OCH CoA hydrolase putative gene was ten times higher in UASB_SL and UASB_LW when compared to UASB_Control, and assigned to Desulfomonile and Syntrophorhabdus. Finally, the adenylylsulfate reductase, taxonomically related with Desulfovibrio and Desulfomonile, was observed in the desulfonation step with the highest relative abundance in UASB_LW.

Metagenomic analysis of the microbiome in three different bioreactor configurations applied to commercial laundry wastewater treatment

The taxonomic and functional diversity of three different biological reactors (fluidized bed reactor, FBR; up-flow anaerobic sludge blanket reactor, UASB; and expanded granular sludge bed reactor, EGSB) used for commercial laundry wastewater treatment was investigated using metagenome shotgun sequencing. Metagenomes were sequenced on the Illumina Hiseq platform and were analyzed using MG-RAST, STAMP and PAST software. The EGSB and UASB reactors were more closely related based on taxonomic and functional profiles, likely due to similar granular sludge and procedures adopted to ensure anaerobic conditions. The EGSB and UASB reactors showed a predominance of methanogens and genes related to methanogenesis, with a prevalence of the acetoclastic pathway, in addition to the peripheral and central O₂-independent pathways for aromatic compound degradation. By contrast, FBR showed a dominance of aerobic microbiota and pathways for O₂-dependent aromatic compound degradation. Therefore, although the reactors showed similar surfactant removal levels, the microbial composition, functional diversity and aromatic compound degradation pathways were significantly distinct.

Evaluation of anionic surfactant removal in anaerobic reactor with Fe(III) supplementation

The objective of this study was to evaluate the removal of linear alkylbenzene sulfonate (LAS) associated with Fe(III) supplementation using an expanded granular sludge bed (EGSB) reactor. The reactor was inoculated with a granular sludge and fed with synthetic wastewater containing a specific LAS load rate (SLLR) of 1.5 mg gVS^-1 d^-1 (∼16.4 mgLAS L^-1 influent) and supplied with 7276 μMol L^-1 of Fe(III). The biomasses from the inoculum and at the end of the EGSB-Fe operation (127 days) were characterized using 16S rRNA Ion Tag sequencing. An increase of 20% in the removal efficiency was observed compared to reactors without Fe(III) supplementation that was reported in the literature, and the LAS removal was approximately 84%. The Fe(III) reduction was dissimilatory (the total iron concentration in the influent and effluent were similar) and reached approximately 64%. The higher Fe(III) reduction and LAS removal were corroborated by the enrichment of genera, such as Shewanella (only EGSB-Fe - 0.5%) and Geobacter (1% - inoculum; 18% - EGSB-Fe). Furthermore, the enrichment of genera that degrade LAS and/or aromatic compounds (3.8% - inoculum; 29.6% - EGSB-Fe of relative abundance) was observed for a total of 20 different genera.

Sulfide-oxidizing bacteria establishment in an innovative microaerobic reactor with an internal silicone membrane for sulfur recovery from wastewater

A novel bioreactor, employing a silicone membrane for microaeration, was studied for partial sulfide oxidation to elemental sulfur. The objective of this study was to assess the feasibility of using an internal silicone membrane reactor (ISMR) to treat dissolved sulfide and to characterize its microbial community. The ISMR is an effective system to eliminate sulfide produced in anaerobic reactors. Sulfide removal efficiencies reached 96 % in a combined anaerobic/microaerobic reactor and significant sulfate production did not occur. The oxygen transfer was strongly influenced by air pressure and flow. Pyrosequencing analysis indicated various sulfide-oxidizing bacteria (SOB) affiliated to the species Acidithiobacillus thiooxidans, Sulfuricurvum kujiense and Pseudomonas stutzeri attached to the membrane and also indicated similarity between the biomass deposited on the membrane wall and the biomass drawn from the material support, supported the establishment of SOB in an anaerobic sludge under microaerobic conditions. Furthermore, these results showed that the reactor configuration can develop SOB under microaerobic conditions and can improve and reestablish the sulfide conversion to elemental sulfur.

Microbial diversity and the implications of sulfide levels in an anaerobic reactor used to remove an anionic surfactant from laundry wastewater

The objective of this study was to evaluate the removal of linear alkylbenzene sulfonate (LAS) from commercial laundry wastewater using an expanded granular sludge bed (EGSB) reactor with two specific LAS loading rates (SLLRs), 1.0 and 2.7 mg LAS gVS(-1)d (-1). The biomass was characterized using denaturing gradient gel electrophoresis (DGGE) and 16S Ion Tag sequencing. Higher LAS removal (92.9%) was observed in association with an SLLR of 1.0 mg LAS gVS(-1) d(-1) than with an SLLR of 2.7 mg LAS gVS(-1) d(-1) (58.6%). A relationship between the S(-2) concentration in the effluent and the surfactant removal efficiency was observed. This result is indicative of the inhibition of LAS-removing microbiota at S(-2) concentrations greater than 20 mg SL(-1). By using DGGE, microbial stratification was observed in the reactor in association with granule size, even though the reactor is considered to be a completely mixed regime. The RDP-classifier identified 175 genera, 33 of which were related to LAS degradation.

The comparative advantages of ethanol and sucrose as co-substrates in the degradation of an anionic surfactant: microbial community selection

The efficiency of linear alkylbenzene sulfonate (LAS) removal from laundry wastewater and the related microbial community was investigated in an anaerobic fluidized bed reactor (AFBR). The AFBR was operated in three stages, in addition to the biomass adaptation stage without LAS (stage I). The stages were differentiated by their supplementary co-substrates: stage II had sucrose plus ethanol, stage III had only ethanol, and stage IV had no co-substrate. The replacement of sucrose plus ethanol with ethanol only for the substrate composition favored the efficiency of LAS removal, which remained high after the co-substrate was removed (stage II: 52 %; stage III: 73 %; stage IV: 77 %). A transition in the microbial community from Comamonadaceae to Rhodocyclaceae in conjunction with the co-substrate variation was observed using ion sequencing analysis. The microbial community that developed in response to an ethanol-only co-substrate improved LAS degradation more than the community that developed in response to a mixture of sucrose and ethanol, suggesting that ethanol is a better option for enriching an LAS-degrading microbial community.

Biodegradation of linear alkylbenzene sulfonate in commercial laundry wastewater by an anaerobic fluidized bed reactor

The biodegradation of linear alkylbenzene sulfonate (LAS) from commercial laundry wastewater was evaluated in an anaerobic fluidized bed reactor (FBR) fed with synthetic substrate (598 mg L(-1) to 723 mg L(-1) of organic matter) supplemented with 9.5±3.1 mg L(-1) to 27.9±9.6 mg L(-1) of LAS. The average chemical oxygen demand (COD) removal efficiency was 89% and the biodegradation of LAS was 57% during the 489 days of anaerobic FBR. Higher levels of volatile fatty acids (VFA) were observed in the effluent at the stage with the best LAS removal performance. Increasing the surfactant concentration did not increase the VFA production in the effluent. The predominant VFAs after the addition of LAS were as follows: isovaleric acid and valeric acid, followed by propionic acid, caproic acid and formic acid. The similarities of 64% and 45% to Archaea and Bacteria domains were observed in the samples taken in the operating period of anaerobic FBR fed with 23.6±10 mg L(-1) and 27.9±10 mg L(-1) of LAS. During the operation stages in the reactor, Gemmatimonas, Desulfobulbus and Zoogloea were determined as the most abundant genera related to surfactant degradation using 454-Pyrosequencing.

Effect of biomass adaptation to the degradation of anionic surfactants in laundry wastewater using EGSB reactors

Two expanded granular sludge bed reactors were operated. RAB (adapted biomass) was operated in two stages: Stage I, with standard LAS (13.2 mg L(-1)); and Stage II, in which the standard LAS was replaced by diluted laundry wastewater according to the LAS concentration (11.2 mg L(-1)). RNAB (not adapted biomass) had a single stage, using direct wastewater (11.5 mg L(-1)). Thus, the strategy of biomass adaptation did not lead to an increase of surfactant removal in wastewater (RAB-Stage II: 77%; RNAB-Stage I: 78%). By means of denaturing gradient gel electrophoresis, an 80% similarity was verified in the phases with laundry wastewater (sludge bed) despite the different reactor starting strategies. By pyrosequencing, many reads were related to genera of degraders of aromatic compounds and sulfate reducers (Syntrophorhabdus and Desulfobulbus). The insignificant difference in LAS removal between the two strategies was most likely due to the great microbial richness of the inoculum.

Influence of volatile fatty acid concentration stability on anaerobic degradation of linear alkylbenzene sulfonate

Linear alkylbenzene sulfonate (LAS) is an anionic surfactant used in cleaning products, which is usually found in wastewaters. Despite the greater LAS removal rate related to a lower concentrations of volatile fatty acids (VFA), the influence of different ranges of VFA on LAS degradation is not known. LAS degradation was evaluated in upflow anaerobic sludge blanket (UASB) and expanded granular sludge bed (EGSB) reactors at different ranges of VFA concentrations. The reactors were fed with a synthetic wastewater containing LAS (14 mg/L). A greater LAS removal rate (40-80%) was related to the lower and narrower range of acetic acid concentration (1-22 mg/L) in the EGSB reactor. In the UASB reactor, the acetic acid concentrations presented a wider range (2-45 mg/L), and some low LAS removal rates (around 20-25%) were observed even at low acetic acid concentrations (<10 mg/L). The high recirculation rate in the EGSB reactor improved substrate-biomass contact, which resulted in a narrower range of VFA and greater LAS removal rate.

Microbial characterization and removal of anionic surfactant in an expanded granular sludge bed reactor

This study evaluated linear alkylbenzene sulfonate removal in an expanded granular sludge bed reactor with hydraulic retention times of 26 h and 32 h. Sludge bed and separator phase biomass were phylogenetically characterized (sequencing 16S rRNA) and quantified (most probable number) to determine the total anaerobic bacteria and methanogenic Archaea. The reactor was fed with a mineral medium supplemented with 14 mg l(-1)LAS, ethanol and methanol. The stage I-32 h consisted of biomass adaptation (without LAS influent) until reactor stability was achieved (COD removal >97%). In stage II-32 h, LAS removal was 74% due to factors such as dilution, degradation and adsorption. Higher HRT values increased the LAS removal (stage III: 26 h - 48% and stage IV: 32 h - 64%), probably due to increased contact time between the biomass and LAS. The clone libraries were different between samples from the sludge bed (Synergitetes and Proteobacteria) and the separator phase (Firmicutes and Proteobacteria) biomass.