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Concept: Anaerobic digestion


ABSTRACT Bacteria and archaea face continual onslaughts of rapidly diversifying viruses and plasmids. Many prokaryotes maintain adaptive immune systems known as clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (Cas). CRISPR-Cas systems are genomic sensors that serially acquire viral and plasmid DNA fragments (spacers) that are utilized to target and cleave matching viral and plasmid DNA in subsequent genomic invasions, offering critical immunological memory. Only 50% of sequenced bacteria possess CRISPR-Cas immunity, in contrast to over 90% of sequenced archaea. To probe why half of bacteria lack CRISPR-Cas immunity, we combined comparative genomics and mathematical modeling. Analysis of hundreds of diverse prokaryotic genomes shows that CRISPR-Cas systems are substantially more prevalent in thermophiles than in mesophiles. With sequenced bacteria disproportionately mesophilic and sequenced archaea mostly thermophilic, the presence of CRISPR-Cas appears to depend more on environmental temperature than on bacterial-archaeal taxonomy. Mutation rates are typically severalfold higher in mesophilic prokaryotes than in thermophilic prokaryotes. To quantitatively test whether accelerated viral mutation leads microbes to lose CRISPR-Cas systems, we developed a stochastic model of virus-CRISPR coevolution. The model competes CRISPR-Cas-positive (CRISPR-Cas+) prokaryotes against CRISPR-Cas-negative (CRISPR-Cas-) prokaryotes, continually weighing the antiviral benefits conferred by CRISPR-Cas immunity against its fitness costs. Tracking this cost-benefit analysis across parameter space reveals viral mutation rate thresholds beyond which CRISPR-Cas cannot provide sufficient immunity and is purged from host populations. These results offer a simple, testable viral diversity hypothesis to explain why mesophilic bacteria disproportionately lack CRISPR-Cas immunity. More generally, fundamental limits on the adaptability of biological sensors (Lamarckian evolution) are predicted. IMPORTANCE A remarkable recent discovery in microbiology is that bacteria and archaea possess systems conferring immunological memory and adaptive immunity. Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (CRISPR-Cas) are genomic sensors that allow prokaryotes to acquire DNA fragments from invading viruses and plasmids. Providing immunological memory, these stored fragments destroy matching DNA in future viral and plasmid invasions. CRISPR-Cas systems also provide adaptive immunity, keeping up with mutating viruses and plasmids by continually acquiring new DNA fragments. Surprisingly, less than 50% of mesophilic bacteria, in contrast to almost 90% of thermophilic bacteria and Archaea, maintain CRISPR-Cas immunity. Using mathematical modeling, we probe this dichotomy, showing how increased viral mutation rates can explain the reduced prevalence of CRISPR-Cas systems in mesophiles. Rapidly mutating viruses outrun CRISPR-Cas immune systems, likely decreasing their prevalence in bacterial populations. Thus, viral adaptability may select against, rather than for, immune adaptability in prokaryotes.

Concepts: Immune system, DNA, Gene, Mutation, Bacteria, Evolution, Genome, Anaerobic digestion


The considerable increase in biodiesel production worldwide in the last 5 years resulted in a stoichiometric increased coproduction of crude glycerol. As an excess of crude glycerol has been produced, its value on market was reduced and it is becoming a “waste-stream” instead of a valuable “coproduct”. The development of biorefineries, i.e. production of chemicals and power integrated with conversion processes of biomass into biofuels, has been singled out as a way to achieve economically viable production chains, valorize residues and coproducts, and reduce industrial waste disposal. In this sense, several alternatives aimed at the use of crude glycerol to produce fuels and chemicals by microbial fermentation have been evaluated. This review summarizes different strategies employed to produce biofuels and chemicals (1,3-propanediol, 2,3-butanediol, ethanol, n-butanol, organic acids, polyols and others) by microbial fermentation of glycerol. Initially, the industrial use of each chemical is briefly presented; then we systematically summarize and discuss the different strategies to produce each chemical, including selection and genetic engineering of producers, and optimization of process conditions to improve yield and productivity. Finally, the impact of the developments obtained until now are placed in perspective and opportunities and challenges for using crude glycerol to the development of biodiesel-based biorefineries are considered. In conclusion, the microbial fermentation of glycerol represents a remarkable alternative to add value to the biodiesel production chain helping the development of biorefineries, which will allow this biofuel to be more competitive.

Concepts: Carbon dioxide, Ethanol, Petroleum, Anaerobic digestion, Biofuel, Glycerol, Biomass, Biodiesel


Microbial anaerobic digestion (AD) is used as a waste treatment process to degrade complex organic compounds into methane. The archaeal and bacterial taxa involved in AD are well known, whereas composition of the fungal community in the process has been less studied. The present study aimed to reveal the composition of archaeal, bacterial and fungal communities in response to increasing organic loading in mesophilic and thermophilic AD processes by applying 454 amplicon sequencing technology. Furthermore, a DNA microarray method was evaluated in order to develop a tool for monitoring the microbiological status of AD.

Concepts: DNA, Archaea, Bacteria, Microbiology, Anaerobic digestion, Methane, Methanogen, Thermophile


Biohydrogen production (BHP) can be achieved by direct or indirect biophotolysis, photo-fermentation and dark fermentation, whereof only the latter does not require the input of light energy. Our motivation to compile this review was to quantify and comprehensively report strains and process performance of dark fermentative BHP. This review summarizes the work done on pure and defined co-culture dark fermentative BHP since the year 1901. Qualitative growth characteristics and quantitative normalized results of H2 production for more than 2000 conditions are presented in a normalized and therefore comparable format to the scientific community.Statistically based evidence shows that thermophilic strains comprise high substrate conversion efficiency, but mesophilic strains achieve high volumetric productivity. Moreover, microbes of Thermoanaerobacterales (Family III) have to be preferred when aiming to achieve high substrate conversion efficiency in comparison to the families Clostridiaceae and Enterobacteriaceae. The limited number of results available on dark fermentative BHP from fed-batch cultivations indicates the yet underestimated potential of this bioprocessing application. A Design of Experiments strategy should be preferred for efficient bioprocess development and optimization of BHP aiming at improving medium, cultivation conditions and revealing inhibitory effects. This will enable comparing and optimizing strains and processes independent of initial conditions and scale.

Concepts: Anaerobic digestion, Motivation, Fermentation, Fermentative hydrogen production, Dark fermentation, Biohydrogen, Photofermentation


Apart from being applied as an energy carrier, hydrogen is in increasing demand as a commodity. Currently, the majority of hydrogen (H2) is produced from fossil fuels, but from an environmental perspective, sustainable H2 production should be considered. One of the possible ways of hydrogen production is through fermentation, in particular, at elevated temperature, i.e. thermophilic biohydrogen production. This short review recapitulates the current status in thermophilic biohydrogen production through fermentation of commercially viable substrates produced from readily available renewable resources, such as agricultural residues. The route to commercially viable biohydrogen production is a multidisciplinary enterprise. Microbiological studies have pointed out certain desirable physiological characteristics in H2-producing microorganisms. More process-oriented research has identified best applicable reactor types and cultivation conditions. Techno-economic and life cycle analyses have identified key process bottlenecks with respect to economic feasibility and its environmental impact. The review has further identified current limitations and gaps in the knowledge, and also deliberates directions for future research and development of thermophilic biohydrogen production.

Concepts: Agriculture, Hydrogen, Research, Anaerobic digestion, Fermentative hydrogen production, Hydrogen production, Dark fermentation, Biohydrogen


The potential of using anaerobic digestion for the treatment of poultry blood has been evaluated in batch assays at the laboratory scale and in a mesophilic semi-continuous reactor. The biodegradability test performed on residual poultry blood was carried out in spite of high inhibitory levels of acid intermediaries. The use of activated carbon as a way to prevent inhibitory conditions demonstrated the feasibility of attaining anaerobic digestion under extreme ammonium and acid conditions. Batch assays with higher carbon content presented higher methane production rates, although the difference in the final cumulative biogas production was not as sharp. The digestion of residual blood was also studied under semi-continuous operation using granular and powdered activated carbon. The average specific methane production was 216 ± 12 mL CH4/g VS. This result was obtained in spite of a strong volatile fatty acid (VFA) accumulation, reaching values around 6 g/L, along with high ammonium concentrations (in the range of 6-8 g/L). The use of powdered activated carbon resulted in a better assimilation of C3-C5 acid forms, indicating that an enhancement in syntrophic metabolism may have taken place. Thermal analysis and scanning electron microscopy (SEM) were applied as analytical tools for measuring the presence of organic material in the final digestate and evidencing modifications on the carbon surface. The addition of activated carbon for the digestion of residual blood highly improved the digestion process. The adsorption capacity of ammonium, the protection this carrier may offer by limiting mass transfer of toxic compounds, and its capacity to act as a conductive material may explain the successful digestion of residual blood as the sole substrate.

Concepts: Protein, Carbon dioxide, Anaerobic digestion, Biogas, Biodegradation, Scanning electron microscope, Methane, Activated carbon


Methane and nitrous oxide are potent greenhouse gases (GHGs) that contribute to climate change. Coastal sediments are important GHG producers, but the contribution of macrofauna (benthic invertebrates larger than 1 mm) inhabiting them is currently unknown. Through a combination of trace gas, isotope, and molecular analyses, we studied the direct and indirect contribution of two macrofaunal groups, polychaetes and bivalves, to methane and nitrous oxide fluxes from coastal sediments. Our results indicate that macrofauna increases benthic methane efflux by a factor of up to eight, potentially accounting for an estimated 9.5% of total emissions from the Baltic Sea. Polychaetes indirectly enhance methane efflux through bioturbation, while bivalves have a direct effect on methane release. Bivalves host archaeal methanogenic symbionts carrying out preferentially hydrogenotrophic methanogenesis, as suggested by analysis of methane isotopes. Low temperatures (8 °C) also stimulate production of nitrous oxide, which is consumed by benthic denitrifying bacteria before it reaches the water column. We show that macrofauna contributes to GHG production and that the extent is dependent on lineage. Thus, macrofauna may play an important, but overlooked role in regulating GHG production and exchange in coastal sediment ecosystems.

Concepts: Carbon dioxide, Bacteria, Baltic Sea, Anaerobic digestion, Natural gas, Methane, Nitrous oxide, Greenhouse gas


Context:Colonization of the gastrointestinal tract with methanogenic archaea (methanogens) significantly affects host metabolism and weight gain in animal models, and breath methane is associated with a greater body mass index (BMI) among obese human subjects.Objective:The objective of the study was to characterize the relationship between methane and hydrogen on breath test (as a surrogate for colonization with the hydrogen requiring methanogen, Methanobrevibacter smithii), body weight, and percent body fat in a general population cohort.Design and Subjects:This was a prospective study (n = 792) of consecutive subjects presenting for breath testing.Setting:The study was conducted at a tertiary care center.Outcome Measurements:BMI and percent body fat were measured.Results:Subjects were classified into 4 groups based on breath testing: normal (N) (methane <3 ppm and hydrogen <20 ppm at or before 90 minutes); hydrogen positive only (H+) [methane <3 ppm and hydrogen ≥20 ppm); methane positive only (M+) (methane ≥3 ppm and hydrogen <20 ppm), or methane and hydrogen positive (M+/H+) (methane ≥3 ppm and hydrogen ≥20 ppm]. There were significant differences in age but not in gender across the groups. After controlling for age as a confounding variable, M+/H+ subjects had significantly higher BMI than other groups (N: 24.1 ± 5.2 kg/m(2); H+: 24.2 ± 4.5 kg/m(2); M+: 24.0 ± 3.75 kg/m(2); M+/H+: 26.5 ± 7.1 kg/m(2), P < .02) and also had significantly higher percent body fat (N: 28.3 ± 10.0%; H+: 27.5 ± 9.0%; M+: 28.0 ± 8.9%; M+/H+; 34.1 ± 10.9%, P < .001).Conclusions:The presence of both methane and hydrogen on breath testing is associated with increased BMI and percent body fat in humans. We hypothesize that this is due to colonization with the hydrogen-requiring M smithii, which affects nutrient availability for the host and may contribute to weight gain.

Concepts: Archaea, Nutrition, Obesity, Mass, Body mass index, Anaerobic digestion, Body weight, Methanogen


This study aimed to evaluate the effects of twenty species of tropical macroalgae on in vitro fermentation parameters, total gas production (TGP) and methane (CH4) production when incubated in rumen fluid from cattle fed a low quality roughage diet. Primary biochemical parameters of macroalgae were characterized and included proximate, elemental, and fatty acid (FAME) analysis. Macroalgae and the control, decorticated cottonseed meal (DCS), were incubated in vitro for 72 h, where gas production was continuously monitored. Post-fermentation parameters, including CH4 production, pH, ammonia, apparent organic matter degradability (OMd), and volatile fatty acid (VFA) concentrations were measured. All species of macroalgae had lower TGP and CH4 production than DCS. Dictyota and Asparagopsis had the strongest effects, inhibiting TGP by 53.2% and 61.8%, and CH4 production by 92.2% and 98.9% after 72 h, respectively. Both species also resulted in the lowest total VFA concentration, and the highest molar concentration of propionate among all species analysed, indicating that anaerobic fermentation was affected. Overall, there were no strong relationships between TGP or CH4 production and the >70 biochemical parameters analysed. However, zinc concentrations >0.10 may potentially interact with other biochemical components to influence TGP and CH4 production. The lack of relationship between the primary biochemistry of species and gas parameters suggests that significant decreases in TGP and CH4 production are associated with secondary metabolites produced by effective macroalgae. The most effective species, Asparagopsis, offers the most promising alternative for mitigation of enteric CH4 emissions.

Concepts: Carbon dioxide, Metabolism, Hydrogen, Concentration, Chemistry, Biochemistry, Anaerobic digestion, Natural gas


Steroid oestrogens (SE) are released by humans and animals into the environment. In the Mekong Delta animal excrement is directly discharged into surface water and can pollute the water. Only a few animal production sites are currently treating the excrement in either biogas plants or vermicomposting systems. The concentration of SE in manures from pigs and cattle was monitored in the Mekong Delta, Vietnam. Fresh cow faeces had an oestrogen concentration of 3.3 ng E2 eq/g dry weight. The SE concentration in effluent from biogas plants fed with animal manures was 341 ng E2 eq/L. Most of the SE were in the solid phase (77.9-98.7%). Vermicomposting reduced SE to 95% of the original input.

Concepts: Photosynthesis, Plant, Cattle, Anaerobic digestion, Feces, Compost, Manure, Cow dung