Obligate sugar oxidation inMesotogaspp., phylumThermotogae, in the presence of either elemental sulfur or hydrogenotrophic sulfate-reducers as electron acceptor

Sulfate-reducing bacteria unearthed: ecological functions of the diverse prokaryotic group in terrestrial environments

Sulfate-reducing prokaryotes (SRPs) are essential microorganisms that play crucial roles in various ecological processes. Even though SRPs have been studied for over a century, there are still gaps in our understanding of their biology. In the past two decades, a significant amount of data on SRP ecology has been accumulated. This review aims to consolidate that information, focusing on SRPs in soils, their relation to the rare biosphere, uncultured sulfate reducers, and their interactions with other organisms in terrestrial ecosystems. SRPs in soils form part of the rare biosphere and contribute to various processes as a low-density population. The data reveal a diverse range of sulfate-reducing taxa intricately involved in terrestrial carbon and sulfur cycles. While some taxa like Desulfitobacterium and Desulfosporosinus are well studied, others are more enigmatic. For example, members of the Acidobacteriota phylum appear to hold significant importance for the terrestrial sulfur cycle. Many aspects of SRP ecology remain mysterious, including sulfate reduction in different bacterial phyla, interactions with bacteria and fungi in soils, and the existence of soil sulfate-reducing archaea. Utilizing metagenomic, metatranscriptomic, and culture-dependent approaches will help uncover the diversity, functional potential, and adaptations of SRPs in the global environment.

Maximizing the energy recovery from rice straw through two-step conversion using eggshell-catalytic pyrolysis followed by enhanced anaerobic digestion using calcium-rich biochar

Anaerobic digestion of lignocelluloses for biogas production is greatly restricted by the poor biomass degradability. Herein, a novel approach is suggested to enhance the energy recovery from rice straw through a two-step conversion using eggshell-based catalytic pyrolysis followed by biochar-based anaerobic co-digestion. Pyrolysis with eggshell significantly enhanced the crude bio-oil yield by 4.6 %. Anaerobic digestion of rice straw using 4 g L^-1 of rice straw biochar (RB) showed the highest recorded biogas yield of 503.7 L kg^-1 VS, with 268.6 L kg^-1 VS biomethane yield. However, 4 g L^-1 of calcium-enriched eggshell rice straw biochar (ERB) enhanced the biomethane yield to 281.8 L kg^-1 VS, which represented 95.6 % higher than the control. It was attributed to enhancement of biomethanation, which resulted in 74.5 % maximum recorded biomethane content at the 7th day of anaerobic digestion. Microbial analysis confirmed that Methanosarciniales was the most dominant Archael group in the control (14.84 %), which increased sharply to 73.91 % and 91.66 % after addition of 4 g L^-1 RB and ERB, respectively. The suggested route enhanced the energy recovery in the form of bio-oil and biomethane by 41.6 %.

Elemental sulphur recovery from a sulphate-rich aqueous stream in a single hybrid linear flow channel reactor is mediated through microbial community dynamics and adaptation to reactor zones

The coupled application of biological sulphate reduction (BSR) and partial sulphide oxidation to treat sulphate-rich wastewater is an effective strategy to mitigate pollution and recover elemental sulphur for repurposing. The recent development of the hybrid linear flow channel reactor (LFCR) achieves simultaneous BSR and partial sulphide oxidation with biosulphur recovery via a floating sulphur biofilm (FSB). Here, we explore the microbial community zoning and dynamics facilitating the process. A total of three continuous LFCRs were used to evaluate the effect of reactor zones, hydraulic residence time (HRT), carbon source, namely lactate and acetate, as well as reactor geometry and scale on process performance and microbial community dynamics. Community composition of sessile and planktonic microbial consortia were resolved at a 5- and 2-day HRT through 16S rRNA amplicon sequencing. Preferential attachment and prevalence of specific phylotypes within the sessile and planktonic communities revealed clear adaptation of key microorganisms to different microenvironments. Key microbial taxa affiliated with sulphate reduction and sulphide oxidation as well as those implicated in fermentation and syntrophic metabolism, fluctuated in response to changes in HRT and process performance. Through understanding the relationship between microbial community dynamics and process performance, this research will inform better process design and optimization of the hybrid LFCR.

Insights into the microbial response mechanisms to ciprofloxacin during sulfur-mediated biological wastewater treatment using a metagenomics approach

The fate and removal of ciprofloxacin, a class of fluoroquinolone antibiotic, during sulfur-mediated biological wastewater treatment has been recently well documented. However, little is known regarding the genetic response of microorganisms to ciprofloxacin. Here, a lab-scale anaerobic sulfate-reducing bioreactor was continuously operated over a long term for ciprofloxacin-contaminated wastewater treatment to investigate the response of the microorganisms to ciprofloxacin by adopting a metagenomics approach. It was found that total organic carbon (TOC) removal and sulfate reduction were promoted by approximately 10% under ciprofloxacin stress, along with the enrichment of functional genera (e.g., Desulfobacter, Geobacter) involved in carbon and sulfur metabolism. The metagenomic analytical results demonstrated that ciprofloxacin triggered the microbial SOS response, as demonstrated by the up-regulation of the multidrug efflux pump genes (8-125-fold higher than that of the control) and ciprofloxacin-degrading genes (4-33-fold higher than that of the control). Moreover, the contents of ATP, NADH, and cytochrome C, as well as related functional genes (including genes involved in energy generation, electron transport, carbon metabolism, and sulfur metabolism) were markedly increased under ciprofloxacin stress. This demonstrated that the carbon and sulfur metabolisms were enhanced for energy (ATP) generation and electron transport in response to ciprofloxacin-induced stress. Interestingly, the microbes tended to cooperate while being subjected exposure to exogenous ciprofloxacin according to the reconstructed metabolic network using the NetSeed model. Particularly, the species with higher complementarity indices played more pivotal roles in strengthening microbial metabolism and the SOS response under long-term ciprofloxacin stress. This study characterized the response mechanisms of microorganisms to ciprofloxacin at the genetic level in sulfur-mediated biological wastewater treatment. These new understandings will contribute the scientific basis for improving and optimizing the sulfur-mediated bioprocess for antibiotics-laden wastewater treatment.

Early-stage response in anaerobic bioreactors due to high sulfate loads: Hydrogen sulfide yield and other organic volatile sulfur compounds as a sign of microbial community modifications

In this work, the early-stage response of six lab-scale biogas bioreactors fed with different amounts of a sulfate-rich organic agro-industrial effluent was investigated. Biogas characterization, gas chromatography selective for sulfur compounds and high-throughput sequencing of 16S rRNA gene were performed. Hydrogen sulfide (H₂S) yield went from transient to steady state in ∼ 2 weeks for all the studied conditions. In addition, volatile sulfur compounds (VSCs), like methanethiol (MeSH) and dimethyl sulfide (DMS), were generated at high sulfate loads. Changes were evidenced in the microbial community structures, with a higher abundance of genes involved in the dissimilatory sulfate-reduction pathway in high loaded sulfate bioreactors, as determined by PICRUSt analysis. Principal component analysis (PCA) and correlation analyses evidenced strong relationships between H₂S, VSCs and the microbial community. Sulfate-reducing bacteria (SRB) like Desulfocarbo, Desulfocella and Desulfobacteraceae might be possibly linked with methylation processes of H₂S.

Dynamic anaerobic membrane bioreactor coupled with sulfate reduction (SrDMBR) for saline wastewater treatment

This study investigated organic removal performance, characteristics of the membrane dynamics, membrane fouling and the effects of biological sulfate reduction during high-salinity (1.0%) and high-sulfate (150 mgSO₄^2--S/L) wastewater treatment using a laboratory-scale upflow anaerobic sludge bed reactor integrated with cross-flow dynamic membrane modules. Throughout the operational period, dynamic membrane was formed rapidly (within 5-10 min) following each backwashing cycle (21-16 days), and the permeate turbidity of <5-7 NTU was achieved with relatively high specific organic conversion (70-100 gTOC/kgVSS·d) and specific sulfate reduction (50-70 gSO₄^2--S/kgVSS·d) rates. The sulfide from sulfate reduction can be reused for downstream autotrophic denitrification. 16S rRNA gene amplicon sequencing revealed that the microbial communities enriched in the sludge were different than those accumulated on the dynamic layer. Overall, this study demonstrates that the anaerobic dynamic membrane bioreactor coupled with sulfate reduction (SrDMBR) shows promising applicability in saline wastewater treatment.

Thermophilic rather than mesophilic sludge anaerobic digesters possess lower antibiotic resistant genes abundance

For exploring the impact of temperature on antibiotic resistant genes (ARGs) during sludge anaerobic digestion (AD), the dynamic variations of sludge ARGs, plasmid ARGs, and cell-free ARGs in mesophilic (25 °C and 35 °C) and thermophilic (55 °C) digesters were investigated. The study revealed that the abundance of sludge ARGs and plasmid ARGs in thermophilic sludge AD was significantly lower than that in mesophilic digesters, while the cell-free ARGs abundance of the thermophilic digesters was similar to mesophilic digesters. Higher archaea abundance, lower bacteria abundance, and different microbial community were found in thermophilic digesters compared to that of mesophilic ones. Firmicutes might be a main group of potential hosts of ARGs in sludge AD. The distinct microbial community was the main contributor to the low ARGs abundance in thermophilic sludge AD. Thermophilic operation at 55 °C rather than mesophilic operation is more conducive to control ARGs in sludge anaerobic digestion.

Effect of Cultivation Parameters on Fermentation and Hydrogen Production in the Phylum Thermotogae

The phylum Thermotogae is composed of a single class (Thermotogae), 4 orders (Thermotogales, Kosmotogales, Petrotogales, Mesoaciditogales), 5 families (Thermatogaceae, Fervidobacteriaceae, Kosmotogaceae, Petrotogaceae, Mesoaciditogaceae), and 13 genera. They have been isolated from extremely hot environments whose characteristics are reflected in the metabolic and phenotypic properties of the Thermotogae species. The metabolic versatility of Thermotogae members leads to a pool of high value-added products with application potentials in many industry fields. The low risk of contamination associated with their extreme culture conditions has made most species of the phylum attractive candidates in biotechnological processes. Almost all members of the phylum, especially those in the order Thermotogales, can produce bio-hydrogen from a variety of simple and complex sugars with yields close to the theoretical Thauer limit of 4 mol H₂/mol consumed glucose. Acetate, lactate, and L-alanine are the major organic end products. Thermotagae fermentation processes are influenced by various factors, such as hydrogen partial pressure, agitation, gas sparging, culture/headspace ratio, inoculum, pH, temperature, nitrogen sources, sulfur sources, inorganic compounds, metal ions, etc. Optimization of these parameters will help to fully unleash the biotechnological potentials of Thermotogae and promote their applications in industry. This article gives an overview of how these operational parameters could impact Thermotogae fermentation in terms of sugar consumption, hydrogen yields, and organic acids production.

Responses to the Hydrostatic Pressure of Surface and Subsurface Strains of Pseudothermotoga elfii Revealing the Piezophilic Nature of the Strain Originating From an Oil-Producing Well

Microorganisms living in deep-oil reservoirs face extreme conditions of elevated temperature and hydrostatic pressure. Within these microbial communities, members of the order Thermotogales are predominant. Among them, the genus Pseudothermotoga is widespread in oilfield-produced waters. The growth and cell phenotypes under hydrostatic pressures ranging from 0.1 to 50 MPa of two strains from the same species originating from subsurface, Pseudothermotoga elfii DSM9442 isolated from a deep African oil-producing well, and surface, P. elfii subsp. lettingae isolated from a thermophilic sulfate-reducing bioreactor, environments are reported for the first time. The data support evidence for the piezophilic nature of P. elfii DSM9442, with an optimal hydrostatic pressure for growth of 20 MPa and an upper limit of 40 MPa, and the piezotolerance of P. elfii subsp. lettingae with growth occurring up to 20 MPa only. Under the experimental conditions, both strains produce mostly acetate and propionate as volatile fatty acids with slight variations with respect to the hydrostatic pressure for P. elfii DSM9442. The data show that the metabolism of P. elfii DSM9442 is optimized when grown at 20 MPa, in agreement with its piezophilic nature. Both Pseudothermotoga strains form chained cells when the hydrostatic pressure increases, especially P. elfii DSM9442 for which 44% of cells is chained when grown at 40 MPa. The viability of the chained cells increases with the increase in the hydrostatic pressure, indicating that chain formation is a protective mechanism for P. elfii DSM9442.

Impact of oxytetracycline on anaerobic wastewater treatment and mitigation using enhanced hydrolysis pretreatment

In this study, two parallel-operated up-flow anaerobic sludge bed reactors, one used to treat synthetic wastewater spiked with oxytetracycline and the other used to treat the same wastewater after enhanced hydrolysis, were used to evaluate the impact of oxytetracycline on anaerobic digestion and resistance development and the efficacy of enhanced hydrolysis pretreatment on the elimination of adverse effects. The reactors were operated under a constant organic-loading rate (10 g/L/d) with increasing oxytetracycline doses (0 mg/L to 200 mg/L) over a period of 15 months. For the reactor without pretreatment, the chemical oxygen demand removal reached up to 89.5%%at oxytetracycline doses ranging from 0 mg/L to 100 mg/L, which collapsed at higher oxytetracycline doses. Miseq sequencing showed that a diverse hydrolysis/fermentation/acetogenesis bacterial community was maintained as the oxytetracycline dose was increased from 0 mg/L to 100 mg/L, while extreme dominance of Macellibacteroides (65.70%%- 71.56%) was found to occur at higher oxytetracycline doses. The total abundance of antibiotic resistance genes increased from 1.3 × 10^-1 copies per cell to 2.6 × 10^-1 copies per cell with increasing oxytetracycline dose from 0 mg/L to 5 mg/L, remained unchanged at oxytetracycline doses ranging from 25 mg/L to 100 mg/L, and then increased to 4.8 × 10^-1 copies per cell and 1.3 copies per cell at oxytetracycline doses of 150 mg/L and 200 mg/L, respectively. Multidrug resistance developed in response to oxytetracycline treatment at 200 mg/L. Poor chemical oxygen demand removal and a marked enrichment in antibiotic resistance genes was validated using a full-scale up-flow anaerobic sludge bed system fed with an influent oxytetracycline concentration of approximately 200 mg/L. For the reactor treating wastewater pretreated with enhanced hydrolysis (85 °C for 6 h), the chemical oxygen demand removal rate and antibiotic resistance genes level over the whole oxytetracycline dose range were found to be similar to those achieved with zero oxytetracycline treatment. These results demonstrated that the control of conventional pollutants and ARGs could be achieved simultaneously in the UASB reactor by employing enhanced hydrolysis pretreatment.

The biomethanation of cow manure in a continuous anaerobic digester can be boosted via a bioaugmentation culture containing Bathyarchaeota

A bioaugmentation approach was used to enhance the performance of anaerobic digestion (AD) using cow manure (CM) as the substrate in a continuous system. To obtain the desirable microbial culture for bioaugmentation, a biochemical methane potential test (BMP) was used to evaluate three commonly used inocula namely (1) municipal solid waste (MSW), (2) wastewater treatment plant (WWTP), and (3) cow manure digester (CMMD) for their hydrolytic capacity. The highest lignocellulose removal (56% for cellulose and 50% for hemicellulose) and the most profusion of cellulolytic bacteria were obtained when CM was inoculated with CMMD. CMMD was thus used as the seed inoculum in a continuously operated reactor (R_a) with the fiber fraction of CM as the substrate to further enrich cellulolytic microbes. After 100 days (HRT: 30 days), the Bacteria fraction mainly contained Ruminofilibacter, norank_o_SBR1031, Treponema, Acetivibrio. Surprisingly, the Archaea fraction contained 97% 'cellulolytic archaea' norank_c_Bathyarchaeia (Phylum Bathyarchaeota). This enriched consortium was used in the bioaugmentation experiment. A positive effect of bioaugmentation was verified, with a substantial daily methane yield (DMY) enhancement (24.3%) obtained in the bioaugmented reactor (R_b) (179 mL CH₄/gVS/d) than that of the control reactor (R_c) (144 mL CH₄/gVS/d) (P < 0.05). Meanwhile, the effluent of R_b enjoyed an improved cellulose reduction (14.7%) than that of R_c, whereas the amount of hemicellulose remained similar in both reactors' effluent. When bioaugmentation stopped, its influence on the hydrolysis and methanogenesis sustained, reflected by an improved DMY (160 mL CH₄/gVS/d) and lower cellulose content (53 mg/g TS) in R_b than those in R_c (DMY 144 mL/CH₄/gVS/d and cellulose content 63 mg/g TS, respectively). The increased DMY of the continuous reactor seeded with a specifically enriched consortium able to degrade the fiber fraction in CM shows the feasibility of applying bioaugmentation in AD of CM.

Elemental sulfur-driven sulfidogenic process under highly acidic conditions for sulfate-rich acid mine drainage treatment: Performance and microbial community analysis

Elemental sulfur-driven sulfidogenic process has been demonstrated to be more economical and energy-efficient than sulfate-driven sulfidogenic process when treating metal-laden wastewater. In previous studies, we observed that the polysulfide-involved indirect sulfur reduction ensured the superiority of sulfur over sulfate as the electron acceptor in the sulfidogenic process under neutral or weak-alkaline conditions. However, realizing high-rate sulfur reduction process for acid mine drainage (AMD) treatment without pH amelioration is still a great challenge because polysulfide cannot exist under acidic conditions. In this study, a laboratory-scale sulfur-packed bed reactor was therefore continuously operated with a constant sulfate concentration (~1300 mg S/L) and decreasing pH from 7.3 to 2.1. After 400 days of operation, a stable sulfide production rate (38.2 ± 7.6 mg S/L) was achieved under highly acidic conditions (pH 2.6-3.5), which is significantly higher than those reported in sulfate reduction under similar conditions. In the presence of high sulfate content, elemental sulfur reduction could dominate over sulfate reduction under neutral and acidic conditions, especially when the pH ≥ 6.5 or ≤ 3.5. The decreasing pH significantly reduced the diversity of microbial community, but did not substantially influence the abundance of functional genes associated with organic and sulfur metabolisms. The predominant sulfur-reducing genera shifted from Desulfomicrobium under neutral conditions to Desulfurella under highly acidic conditions. The high-rate sulfur reduction under acidic conditions could be attributed to the combined results of high abundance of Desulfurella and low abundance of sulfate-reducing bacteria (SRB). Accordingly, sulfur reduction process can be developed to achieve efficient and economical treatment of AMD under highly acidic conditions (pH ≤ 3.5).

Microbial interactions regulated by the dosage of ferroferric oxide in the co-metabolism of organic carbon and sulfate

Effects of ferroferric oxide (Fe₃O₄) and organic carbon on co-metabolism of sulfate and organic carbon were investigated. With Fe₃O₄, the degradation of acetate and sulfate was inhibited when fed with acetate, while the degradation of acetate and propionate produced from ethanol was promoted when fed with ethanol. The dominant sulfate reducing bacteria (SRB) of acetate-fed reactors were Desulfobacteraceae (complete oxidizing SRB, CO-SRB) and Desulfurmonas (incomplete oxidizing SRB, IO-SRB). IO-SRBs of Desulfobulbus and Desulfomicrobium were dominant in ethanol-fed reactors. CO-SRB had higher competitiveness than methanogens to utilize acetate, while IO-SRBs might cooperate with methanogens to produce methane when dosed with ethanol and Fe₃O₄. The dosage of Fe₃O₄ changed the dominant methanogen from Methanosarcina to Methanosaeta with acetate as the organic carbon, while increased the relative abundance of Methanosaeta with ethanol as the organic carbon.

Co-feeding spent coffee grounds in anaerobic food waste digesters: Effects of co-substrate and stabilization strategy

Anaerobic digestion of spent coffee grounds (SCG) is considered disadvantageous, particularly under mono-digestion conditions, owing to slow degradation and nutrient imbalance. This study investigated the effect of co-feeding of SCG at a low ratio into food waste (FW) digesters, with the aim to determine whether SCG can be effectively treated and valorized using the spare capacity of existing digesters. Duplicate reactors showed stable performance under FW mono-digestion conditions but manifested severe deterioration in three volume turnovers after co-feeding of SCG (FW:SCG at 10:1 on a volatile solids basis). The reactors failed to recover despite repeated interrupted feeding and stabilization, and Ulva was added (FW:SCG:Ulva at 20:2:1) for nutrient supplementation. The two reactors subjected to different stabilization strategies (i.e., timing and intervals of interrupted feeding) responded differently to Ulva co-feeding: one recovered and maintained stable albeit suboptimal performance, whereas the other failed. Furthermore, the microbial communities developed differently in the reactors.

Evaluation of phase separation in a single-stage vertical anaerobic reactor: Performance and microbial composition analysis

In order to explore whether the acidogenic phase and methanogenic phase could be separated vertically into a single-stage anaerobic reactor, a controlled double circulation (CDC) anaerobic reactor was proposed for treating traditional Chinese medicine (TCM) wastewater in this study. The results showed that most of the organic pollutants and refractory were removed in the first reaction area where most of the amount of sludge existed. The organic acids were accumulated in the first reaction area, and larger specific methanogenic activity (SMA) and coenzyme F₄₂₀ values were found in the second reaction area. Bacterial and archaeal community structures in the two reaction areas of the CDC reactor were analyzed by Illumina MiSeq Sequencing, which revealed that the archaeal community showed larger difference compared with the bacterial community. Differences in the performance and microbial composition of the two reaction areas confirmed that phase separation was implemented in the CDC reactor.