Effect of dissolved solids released from biochar on soil microbial metabolism

Dissolved solids released from biochar (DSRB), including organic and inorganic compounds, may affect the role of biochar as a soil amendment. In this study, the effects of DSRB on soil microbe metabolism, especially CO₂ fixation, were evaluated in liquid soil extract. DSRB were found to be released in large amounts (289.05 mg L^-1 at 1 hour) from biochar over a short period of time before their rate of release slowed to a gradual pace. They increased the microbial biomass and provided energy and reducing power to microbes, while reducing their metabolic output of extracellular proteins and polysaccharides. DSRB inputs led to the redistribution of metabolic flux in soil microorganisms and an increased organic carbon content in the short term. This content gradually decreased as it was utilized. DSRB did not improve microbial CO₂ fixation but, rather, enhanced its release, while promoting specific soil microorganism genera, including Cupriavidus, Flavisolibacter, and Pseudoxanthomonas. These heterotrophic genera may compete with autotrophic microorganisms for nutrients but have positive synergistic relationships with autotrophs during CO₂ fixation. These results demonstrated that reducing the DSRB in biochar can improve its role as a soil amendment by enhancing soil carbon storage and CO₂ fixation capabilities.

Directed Evolution of Microbial Communities

Directed evolution is a form of artificial selection that has been used for decades to find biomolecules and organisms with new or enhanced functional traits. Directed evolution can be conceptualized as a guided exploration of the genotype-phenotype map, where genetic variants with desirable phenotypes are first selected and then mutagenized to search the genotype space for an even better mutant. In recent years, the idea of applying artificial selection to microbial communities has gained momentum. In this article, we review the main limitations of artificial selection when applied to large and diverse collectives of asexually dividing microbes and discuss how the tools of directed evolution may be deployed to engineer communities from the top down. We conceptualize directed evolution of microbial communities as a guided exploration of an ecological structure-function landscape and propose practical guidelines for navigating these ecological landscapes.

Uncovering microbial responses to sharp geochemical gradients in a terrace contaminated by acid mine drainage

Acid mine drainage (AMD) is harmful to the environment and human health. Microorganisms-mineral interactions are responsible for AMD generation but can also remediate AMD contamination. Understanding the microbial response to AMD irrigation will reveal microbial survival strategies and provide approaches for AMD remediation. A terrace with sharp geochemical gradients caused by AMD flooding were selected to study the microbial response to changes in environmental parameters related to AMD contamination. AMD intrusion reduced soil microbial community diversity and further changed phylogenetic clustering patterns along the terrace gradient. We observed several genera seldom reported in AMD-related environments (i.e., Corynebacterium, Ochrobactrum, Natronomonas), suggesting flexible survival strategies such as nitrogen fixation, despite the poor nutritional environment. A co-occurrence network of heavily-contaminated fields was densely connected. The phyla Proteobacteria, Acidobacteria, Chloroflexi, and Euryarchaeota were all highly interconnected members, which may affect the formation of AMD. Detailed microbial response to different soil characterizations were highlighted by random forest model. Results revealed the top three parameters influencing the microbial diversity and interactions were pH, Fe(III), and sulfate. Various acidophilic Fe- and S-metabolizing bacteria were enriched in the lower fields, which were heavily contaminated by AMD, and more neutrophiles prevailed in the less-contaminated upper fields. Many indicator species in the lower fields were identified, including Desulfosporosinus, Thermogymnomonas, Corynebacterium, Shewanella, Acidiphilium, Ochrobactrum, Leptospirillum, and Allobaculum, representing acid-tolerant bacteria community in relevant environment. The detection of one known sulfate-reducing bacteria (i.e., Desulfosporosinus) suggested that biotic sulfate reduction may occur in acidic samples, which offers multiple advantages to AMD contamination treatment. Collectively, results suggested that the geochemical gradients substantially altered the soil microbiota and enriched the relevant microorganisms adapted to the different conditions. These findings provide mechanistic insights into the effects of contamination on the soil microbiota and establish a basis for in situ AMD bioremediation strategies.

Microbial community design: methods, applications, and opportunities

Microbial communities can perform a variety of behaviors that are useful in both therapeutic and industrial settings. Engineered communities that differ in composition from naturally occurring communities offer a unique opportunity for improving upon existing community functions and expanding the range of microbial community applications. This has prompted recent advances in various community design approaches including artificial selection procedures, reduction from existing communities, combinatorial evaluation of potential microbial combinations, and model-based in silico community optimization. Computational methods in particular offer a likely avenue toward improved synthetic community development going forward. This review introduces each class of design approach and surveys their recent applications and notable innovations, closing with a discussion of existing design challenges and potential opportunities for advancement.

Utilization of the saccharification residue of rice straw in the preparation of biochar is a novel strategy for reducing CO2 emissions

Once rice straw has been bioconverted into biofuels, it is difficult to further biodegrade or decompose the saccharification residue (mainly lignin). Taking into account the pyrolysis characteristics of lignin, in this study the saccharification residue was used as a raw material for the preparation of biochar (biochar-SR), a potential soil amendment. Biochar was prepared directly from rice straw (biochar-O) with a yield of 32.45 g/100 g rice straw, whereas 30.14 g biochar-SR and 30.46 g monosaccharides (including 20.46 g glucose, 9.11 g xylose, and 0.89 g arabinose) were obtained from 100 g of rice straw. When added to liquid soil extracts as a soil amendment, almost nothing was released from biochar-SR, whereas numerous dissolved solids (about 70 mg/L) were released from biochar-O. Adding a mixture of biochar-SR and autotrophic bacteria improved soil total organic carbon 1.8-fold and increased the transcription levels of cbbL and cbbM, which were 4.76 × 10³ and 3.76 × 10⁵ times those of the initial blank, respectively. By analyzing the soil microbial community, it was clear that the above mixture favored the growth of CO₂-fixing bacteria such as Ochrobactrum. Compared with burning rice straw or preparing biochar-O, the preparation of biochar-SR reduced CO₂ emissions by 67.53% or 37.13%, respectively. These results demonstrate that biochar-SR has potential applications in reducing the cost of sustainable energy and addressing environmental issues.

DNA-SIP Reveals the Diversity of Chemolithoautotrophic Bacteria Inhabiting Three Different Soil Types in Typical Karst Rocky Desertification Ecosystems in Southwest China

Autotrophs that inhabit soils receive less attention than their counterparts in other ecosystems, such as deep-sea and subsurface sediments, due to the low abundance of autotrophs in soils with high organic contents. However, the karst rocky desertification region is a unique ecosystem that may have a low level of organic compounds. Therefore, we propose that karst rocky desertification ecosystems may harbor diverse autotrophic microbial communities. In this study, DNA-SIP was employed to identify the chemolithoautotrophic bacteria inhabiting three soil types (i.e., grass, forest, and agriculture) of the karst rocky desertification ecosystems. The results indicated that potential chemolithoautotrophic population was observed in each soil type, even at different time points after amending ¹³C-NaHCO₃, confirming our hypothesis that diverse autotrophs contribute to the carbon cycle in karst soils. Bacteria, such as Ralstonia, Ochrobactrum, Brevibacterium, Acinetobacter, and Corynebacterium, demonstrated their potential to assimilate inorganic carbon and reduce nitrate or thiosulfate as electron acceptors. Putative mixotrophs were identified by DNA-SIP as well, suggesting the metabolic versatility of soil microbiota. A co-occurrence network further indicated that autotrophs and heterotrophs may form associated communities to sustain the ecosystem function. Our current study revealed the metabolic diversity of autotrophic bacteria in soil habitats and demonstrated the potentially important role of chemoautotrophs in karst rocky desertification ecosystems.

Trends, application and future prospectives of microbial carbonic anhydrase mediated carbonation process for CCUS

Growing industrialization and the desire for a better economy in countries has accelerated the emission of greenhouse gases (GHGs), by more than the buffering capacity of the earth's atmosphere. Among the various GHGs, carbon dioxide occupies the first position in the anthroposphere and has detrimental effects on the ecosystem. For decarbonization, several non-biological methods of carbon capture, utilization and storage (CCUS) have been in use for the past few decades, but they are suffering from narrow applicability. Recently, CO₂ emission and its disposal related problems have encouraged the implementation of bioprocessing to achieve a zero waste economy for a sustainable environment. Microbial carbonic anhydrase (CA) catalyses reversible CO₂ hydration and forms metal carbonates that mimic the natural phenomenon of weathering/carbonation and is gaining merit for CCUS. Thus, the diversity and specificity of CAs from different micro-organisms could be explored for CCUS. In the literature, more than 50 different microbial CAs have been explored for mineral carbonation. Further, microbial CAs can be engineered for the mineral carbonation process to develop new technology. CA driven carbonation is encouraging due to its large storage capacity and favourable chemistry, allowing site-specific sequestration and reusable product formation for other industries. Moreover, carbonation based CCUS holds five-fold more sequestration capacity over the next 100 years. Thus, it is an eco-friendly, feasible, viable option and believed to be the impending technology for CCUS. Here, we attempt to examine the distribution of various types of microbial CAs with their potential applications and future direction for carbon capture. Although there are few key challenges in bio-based technology, they need to be addressed in order to commercialize the technology.

Design and composition of synthetic fungal-bacterial microbial consortia that improve lignocellulolytic enzyme activity

Microbial interactions are important for metabolism as they can improve or reduce metabolic efficiency. To improve lignocellulolytic enzyme activity, a series of synergistic microbial consortia of increasing diversity and complexity were devised using fungal strains, including Trichoderma reesei, Penicillium decumbens, Aspergillus tubingensis, and Aspergillus niger. However, when a screened microbial community with cellulolytic capacity was added to the consortia to increase the number of strains, it engendered more microbial interactions with the above strains and universally improved the β-glucosidase activity of the consortia. Analysis of the microbial community structure revealed that the bacteria in the consortia are more important for lignocellulolytic enzyme activity than the fungi. One fungal and 16 bacterial genera in the consortia may interact with T. reesei and are potential members of a devised synergistic microbial consortium. Such devised microbial consortia may potentially be applied to effectively and economically degrade lignocellulose.