Photo‐switchable microbial fuel‐cells

Regulation of Bio‐systems in a clean, simple, and efficient way is important for the design of smart bio‐interfaces and bioelectronic devices. Light as a non‐invasive mean to control the activity of a protein enables spatial and temporal control far superior to other chemical and physical methods. The ability to regulate the activity of a catalytic enzyme in a biofuel‐cell reduces the waste of resources and energy and turns the fuel‐cell into a smart and more efficient device for power generation. Here we present a microbial‐fuel‐cell based on a surface displayed, photo‐switchable alcohol dehydrogenase. The enzyme was modified near the active site using non‐canonical amino acids and a small photo‐reactive molecule, which enables reversible control of enzymatic activity. Depending on the modification site, the enzyme exhibits reversible behavior upon irradiation with UV and visible light, in both biochemical, and electrochemical assays. The change observed in power output of a microbial fuel cell utilizing the modified enzyme was almost five‐fold, between inactive and active states.     

Temperature sensitivity of biomass‐specific microbial exo‐enzyme activities and CO2 efflux is resistant to change across short‐ and long‐term timescales

Accurate representation of temperature sensitivity (Q₁₀) of soil microbial activity across time is critical for projecting soil CO₂ efflux. As microorganisms mediate soil carbon (C) loss via exo‐enzyme activity and respiration, we explore temperature sensitivities of microbial exo‐enzyme activity and respiratory CO₂ loss across time and assess mechanisms associated with these potential changes in microbial temperature responses. We collected soils along a latitudinal boreal forest transect with different temperature regimes (long‐term timescale) and exposed these soils to laboratory temperature manipulations at 5, 15, and 25°C for 84 days (short‐term timescale). We quantified temperature sensitivity of microbial activity per g soil and per g microbial biomass at days 9, 34, 55, and 84, and determined bacterial and fungal community structure before the incubation and at days 9 and 84. All biomass‐specific rates exhibited temperature sensitivities resistant to change across short‐ and long‐term timescales (mean Q₁₀ = 2.77 ± 0.25, 2.63 ± 0.26, 1.78 ± 0.26, 2.27 ± 0.25, 3.28 ± 0.44, 2.89 ± 0.55 for β‐glucosidase, N‐acetyl‐β‐d ‐glucosaminidase, leucine amino peptidase, acid phosphatase, cellobiohydrolase, and CO₂ efflux, respectively). In contrast, temperature sensitivity of soil mass‐specific rates exhibited either resilience (the Q₁₀ value changed and returned to the original value over time) or resistance to change. Regardless of the microbial flux responses, bacterial and fungal community structure was susceptible to change with temperature, significantly differing with short‐ and long‐term exposure to different temperature regimes. Our results highlight that temperature responses of microbial resource allocation to exo‐enzyme production and associated respiratory CO₂ loss per unit biomass can remain invariant across time, and thus, that vulnerability of soil organic C stocks to rising temperatures may persist in the long term. Furthermore, resistant temperature sensitivities of biomass‐specific rates in spite of different community structures imply decoupling of community constituents and the temperature responses of soil microbial activities.     

Above‐ and belowground linkages in Sphagnum peatland: climate warming affects plant‐microbial interactions

Peatlands contain approximately one third of all soil organic carbon (SOC). Warming can alter above‐ and belowground linkages that regulate soil organic carbon dynamics and C‐balance in peatlands. Here we examine the multiyear impact of in situ experimental warming on the microbial food web, vegetation, and their feedbacks with soil chemistry. We provide evidence of both positive and negative impacts of warming on specific microbial functional groups, leading to destabilization of the microbial food web. We observed a strong reduction (70%) in the biomass of top‐predators (testate amoebae) in warmed plots. Such a loss caused a shortening of microbial food chains, which in turn stimulated microbial activity, leading to slight increases in levels of nutrients and labile C in water. We further show that warming altered the regulatory role of Sphagnum‐polyphenols on microbial community structure with a potential inhibition of top predators. In addition, warming caused a decrease in Sphagnum cover and an increase in vascular plant cover. Using structural equation modelling, we show that changes in the microbial food web affected the relationships between plants, soil water chemistry, and microbial communities. These results suggest that warming will destabilize C and nutrient recycling of peatlands via changes in above‐ and belowground linkages, and therefore, the microbial food web associated with mosses will feedback positively to global warming by destabilizing the carbon cycle. This study confirms that microbial food webs thus constitute a key element in the functioning of peatland ecosystems. Their study can help understand how mosses, as ecosystem engineers, tightly regulate biogeochemical cycling and climate feedback in peatlands     

T‐RFLP reveals high β‐Proteobacteria diversity in microbial fuel cells enriched with domestic wastewater

Aims: To assess the biodiversity of a large number of microbial fuel cell (MFC) anodes from a variety of MFC designs, all enriched with domestic wastewater, using a molecular fingerprinting method. Methods and Results: We optimized a protocol allowing the rapid characterization of MFC communities using terminal restriction fragment length polymorphism (T‐RFLP) with two different sets of primers and a varying number of restriction enzymes. This protocol was further validated by direct comparison with bacterial clone libraries. Twenty‐one MFC anodes were analysed by T‐RFLP. We also provided a statistical comparison with other bacterial communities from environments sharing common features. Conclusions: Bacterial communities were dominated by β‐Proteobacteria, mostly belonging to the Burkholderiales order, that are known to play an active role in the cycle of metals such as iron and manganese. This property may allow them to properly pass electrons to the anode of an MFC. Significance and Impact of the Study: Unlike other groups, β‐Proteobacteria have seldom been acknowledged as potentially efficient electrochemically active bacteria (EAB) in MFCs. Yet, they are plentiful in natural environments like biocorrosion biofilms and acid mine drainages that consequently show some potential for MFC enrichment.     

GeoChip 4: a functional gene‐array‐based high‐throughput environmental technology for microbial community analysis

Micro‐organisms play critical roles in many important biogeochemical processes in the Earth's biosphere. However, understanding and characterizing the functional capacity of microbial communities are still difficult due to the extremely diverse and often uncultivable nature of most micro‐organisms. In this study, we developed a new functional gene array, GeoChip 4, for analysing the functional diversity, composition, structure, metabolic potential/activity and dynamics of microbial communities. GeoChip 4 contained approximately 82 000 probes covering 141 995 coding sequences from 410 functional gene families related to microbial carbon (C), nitrogen (N), sulphur (S), and phosphorus (P) cycling, energy metabolism, antibiotic resistance, metal resistance/reduction, organic remediation, stress responses, bacteriophage and virulence. A total of 173 archaeal, 4138 bacterial, 404 eukaryotic and 252 viral strains were targeted, providing the ability to analyse targeted functional gene families of micro‐organisms included in all four domains. Experimental assessment using different amounts of DNA suggested that as little as 500 ng environmental DNA was required for good hybridization, and the signal intensities detected were well correlated with the DNA amount used. GeoChip 4 was then applied to study the effect of long‐term warming on soil microbial communities at a Central Oklahoma site, with results indicating that microbial communities respond to long‐term warming by enriching carbon degradation, nutrient cycling (nitrogen and phosphorous) and stress response gene families. To the best of our knowledge, GeoChip 4 is the most comprehensive functional gene array for microbial community analysis.     

Control of microbial attachment by inhibition of ATP and ATP‐mediated autoinducer‐2

In this study, 2,4‐dinitrophenol (DNP), a typical chemical uncoupler, was employed to investigate the possible roles of ATP and autoinducer‐2 (AI‐2) of suspended microorganisms in attachment onto nylon membrane and glass slide surfaces. Results showed that DNP could disrupt ATP synthesis, subsequently led to a reduced production of AI‐2 which is a common signaling molecule for cellular communication. Attachment of suspended microorganisms exposed to DNP was significantly suppressed as compared to microorganisms without contact with DNP. These suggest that an energized state of suspended microorganisms would favor microbial attachment to both nylon membrane and glass slide surfaces. The extent of microbial attachment was found to be positively related to the AI‐2 content of microorganisms. This study offers insights into the control of biofouling by preventing initial microbial attachment through inhibition of energy metabolism. Biotechnol. Bioeng. 2010;107: 31–36. © 2010 Wiley Periodicals, Inc.     

Linking microbial co‐occurrences to soil ecological processes across a woodland‐grassland ecotone

Ecotones between distinct ecosystems have been the focus of many studies as they offer valuable insights into key drivers of community structure and ecological processes that underpin function. While previous studies have examined a wide range of above‐ground parameters in ecotones, soil microbial communities have received little attention. Here we investigated spatial patterns, composition, and co‐occurrences of archaea, bacteria, and fungi, and their relationships with soil ecological processes across a woodland‐grassland ecotone. Geostatistical kriging and network analysis revealed that the community structure and spatial patterns of soil microbiota varied considerably between three habitat components across the ecotone. Woodland samples had significantly higher diversity of archaea while the grassland samples had significantly higher diversity of bacteria. Microbial co‐occurrences reflected differences in soil properties and ecological processes. While microbial networks were dominated by bacterial nodes, different ecological processes were linked to specific microbial guilds. For example, soil phosphorus and phosphatase activity formed the largest clusters in their respective networks, and two lignolytic enzymes formed joined clusters. Bacterial ammonia oxidizers were dominant over archaeal oxidizers and showed a significant association (p < 0.001) with potential nitrification (PNR), with the PNR subnetwork being dominated by Betaproteobacteria. The top ten keystone taxa comprised six bacterial and four fungal OTUs, with Random Forest Analysis revealing soil carbon and nitrogen as the determinants of the abundance of keystone taxa. Our results highlight the importance of assessing interkingdom associations in soil microbial networks. Overall, this study shows how ecotones can be used as a model to delineate microbial structural patterns and ecological processes across adjoining land‐uses within a landscape.     

Short‐term temperature change may impact freshwater carbon flux: a microbial perspective

Small freshwater bodies are abundant and economically and ecologically important on a global scale. Within these, protozoa play an important role in structuring planktonic food webs and sequestering CO₂. We hypothesized that short‐term (～20 days) fluctuations, of 2–10 °C, will significantly alter carbon flux associated with predator–prey interactions within the microbial planktonic food web. We examined the model ciliate, Urotricha farcta, which is abundant and common; it was fed the autotrophic flagellate Cryptomonas sp., which is also common. Laboratory experiments were conducted over relevant ranges: 8–24 °C; 0–2 × 10⁵ prey mL^?1. Mechanistic‐phenomenological multiple regressions were developed and fit to the data to obtain relationships for (1) growth rate and volume changes of the flagellate vs. temperature and (2) growth rates, grazing, and cell volume change of the ciliate vs. temperature and prey concentration. Responses revealed interaction between temperature and prey levels on all ciliate parameters, indicating it is inappropriate to apply simple temperature corrections (e.g. Q₁₀) to such functions. The potential impact of such temperature changes on carbon flux was illustrated using a simple ciliate–flagellate predator–prey model, with and without the top grazer, Daphnia, added. The model indicated that predator–prey pulses occurred over 20 days, with the ciliate controlling the prey population. For ciliates and prey, carbon production peaked at 20 °C and rapidly decreased above and below this maximum; differences between minimum and maximum were approximately fourfold, for both prey and ciliate, with low levels at 25–30 °C and 10–15 °C. Including literature data to parameterize, the influence of the grazer Daphnia did not alter the prediction that the ciliate may control short‐term flagellate pulses and temperature will influence these in a nonintuitive fashion.     

Millimeter‐scale genetic gradients and community‐level molecular convergence in a hypersaline microbial mat

To investigate the extent of genetic stratification in structured microbial communities, we compared the metagenomes of 10 successive layers of a phylogenetically complex hypersaline mat from Guerrero Negro, Mexico. We found pronounced millimeter‐scale genetic gradients that were consistent with the physicochemical profile of the mat. Despite these gradients, all layers displayed near‐identical and acid‐shifted isoelectric point profiles due to a molecular convergence of amino‐acid usage, indicating that hypersalinity enforces an overriding selective pressure on the mat community.     

Effects of forest degradation on microbial communities and soil carbon cycling: A global meta‐analysis

Aim

The aim was to explore how conversions of primary or secondary forests to plantations or agricultural systems influence soil microbial communities and soil carbon (C) cycling.

Location

Global.

Time period

1993–2017.

Major taxa studied

Soil microbes.

Methods

A meta‐analysis was conducted to examine effects of forest degradation on soil properties and microbial attributes related to microbial biomass, activity, community composition and diversity based on 408 cases from 119 studies in the world.

Results

Forest degradation decreased the ratios of K‐strategists to r‐strategists (i.e., ratios of fungi to bacteria, Acidobacteria to Proteobacteria, Actinobacteria to Bacteroidetes and Acidobacteria + Actinobacteria to Proteobacteria + Bacteroidetes). The response ratios (RRs) of the K‐strategist to r‐strategist ratios to forest degradation decreased and increased with increased RRs of soil pH and soil C to nitrogen ratio (C:N), respectively. Forest degradation increased the bacterial alpha‐diversity indexes, of which the RRs increased and decreased as the RRs of soil pH and soil C:N increased, respectively. The overall RRs across all the forest degradation types ranked as microbial C (?40.4%) > soil C (?33.3%) > microbial respiration (?18.9%) > microbial C to soil C ratio (qMBC; ?15.9%), leading to the RRs of microbial respiration rate per unit microbial C (qCO₂) and soil C decomposition rate (respiration rate per unit soil C), on average, increasing by +43.2 and +25.0%, respectively. Variances of the RRs of qMBC and qCO₂ were significantly explained by the soil C, soil C:N and mean annual precipitation.

Main conclusions

Forest degradation consistently shifted soil microbial community compositions from K‐strategist dominated to r‐strategist dominated, altered soil properties and stimulated microbial activity and soil C decomposition. These results are important for modelling the soil C cycling under projected global land‐use changes and provide supportive evidence for applying the macroecology theory on ecosystem succession and disturbance in soil microbial ecology.     

Co‐utilization of acidified glycerol pretreated‐sugarcane bagasse for microbial oil production by a novel Rhodosporidium strain

Acidified glycerol pretreatment is very effective to deconstruct lignocellulosics for producing glucose. Co‐utilization of pretreated biomass and residual glycerol to bioproducts could reduce the costs associated with biomass wash and solvent recovery. In this study, a novel strain Rhodosporidium toruloides RP 15, isolated from sugarcane bagasse, was selected and tested for coconversion of pretreated biomass and residual glycerol to microbial oils. In the screening trails, Rh. toruloides RP 15 demonstrated the highest oil production capacity on glucose, xylose, and glycerol among the 10 strains. At the optimal C:N molar ratio of 140:1, this strain accumulated 56.7, 38.3, and 54.7% microbial oils based on dry cell biomass with 30 g/L glucose, xylose, and glycerol, respectively. Furthermore, sugarcane bagasse medium containing 32.6 g/L glucose from glycerol‐pretreated bagasse and 23.4 g/L glycerol from pretreatment hydrolysate were used to produce microbial oils by Rh. toruloides RP 15. Under the preliminary conditions without pH control, this strain produced 7.7 g/L oil with an oil content of 59.8%, which was comparable or better than those achieved with a synthetic medium. In addition, this strain also produced 3.5 mg/L carotenoid as a by‐product. It is expected that microbial oil production can be significantly improved through process optimization.     

Establishing microbial co‐cultures for 3‐hydroxybenzoic acid biosynthesis on glycerol

Converting renewable feedstocks to aromatic compounds using engineered microbes offers a robust approach for sustainable, environment‐friendly, and cost‐effective production of these value‐added products without the reliance on petroleum. In this study, rationally designed E. coli–E. coli co‐culture systems were established for converting glycerol to 3‐hydroxybenzoic acid (3HB). Specifically, the 3HB pathway was modularized and accommodated by two metabolically engineered E. coli strains. The co‐culture biosynthesis was optimized by using different cultivation temperatures, varying the inoculum ratio between the co‐culture strains, recruitment of a key pathway intermediate transporter, strengthening the critical pathway enzyme expression, and adjusting the timing for inducing pathway gene expression. Compared with the E. coli mono‐culture, the optimized co‐culture showed 5.3‐fold improvement for 3HB biosynthesis. This study demonstrated the applicability of modular co‐culture engineering for addressing the challenges of aromatic compound biosynthesis.     

Partial incubation during egg laying reduces eggshell microbial loads in a temperate‐breeding passerine

Incubation prior to clutch completion may be adaptive if it maintains egg viability by inhibiting eggshell microbial growth, thus reducing the likelihood that the embryo becomes infected. To test this hypothesis, we examined the effect of partial incubation during egg laying on eggshell microbial loads in eastern bluebirds Sialia sialis breeding at a temperate‐zone site. We sampled eggshell microbes prior to and following four days of exposure to either partial incubation during the laying period or ambient environmental conditions without incubation (experimental eggs). Microbial colony counts declined significantly for eggs left in the nest during the laying period but did not vary significantly for eggs exposed to ambient conditions. Initial microbial loads were more similar to those previously reported from tropical than temperate environments, and microbes from potentially pathogenic groups were detected on 88% of first‐laid eggs on the day of laying. Egg viability was maintained when eggs were held indoors for four days without incubation but declined sharply thereafter. Our results suggest that partial incubation during egg laying may enhance egg viability in eastern bluebirds by reducing eggshell microbial loads; these effects appear stronger than those usually reported from the temperate zone.     

Thermophilic enrichment of microbial communities in the presence of the ionic liquid 1‐ethyl‐3‐methylimidazolium acetate

Aims

The aim of the study was to develop an approach to enrich ionic liquid tolerant micro‐organisms that efficiently decompose lignocellulose in a thermophilic and high‐solids environment.

Methods and Results

High‐solids incubations were conducted, using compost as an inoculum source, to enrich for thermophilic communities that decompose switchgrass in the presence of the ionic liquid 1‐ethyl‐3‐methylimidazolium acetate ([C2mim][OAc]). Ionic liquid levels were increased from 0 to 6% on a total weight basis incrementally. Successful enrichment of a community that decomposed lignocellulose at 55°C in the presence of 6% [C2mim][OAc] was achieved, when the [C2mim][OAc] level was increased stepwise from 2% to 4% to 5% to 6%. Pyrosequencing results revealed a shift in the community and a sharp decrease in richness, when thermophilic conditions were applied.

Conclusions

A community tolerant to a thermophilic, high‐solids environment containing 6% [C2mim][OAc] was enriched from compost. Gradually increasing [C2mim][OAc] concentrations allowed the community to adapt to [C2mim][OAc].

Significance and Impact of the Study

A successful approach to enrich communities that decompose lignocellulose under thermophilic high‐solids conditions in the presence of elevated levels of [C2mim][OAc] has been developed. Communities yielded from this approach will provide resources for the discovery of enzymes and metabolic pathways relevant to biomass pretreatment and fuel production.     

Oxygen availability effect on the performance of air‐breathing cathode microbial fuel cell

The effect of the oxygen availability over the performance of an air‐breathing microbial fuel cell (MFC) was studied by limiting the oxygen supply to the cathode. It was found that anodic reaction was the limiting stage in the performance of the MFC while oxygen was fully available at cathode. As the cathode was depleted of oxygen, the current density becomes limited by oxygen transport to the electrode surface. The exerted current density was maintained when oxygen mole fraction was higher than 10% due to the very good performance of the cathodic catalysts. However, the current density drastically falls when working at lower concentrations because of mass transfer limitations. In this sense it must be highlighted that the maximum exerted power, when oxygen mole fraction was higher than 10%, was almost three times higher than that obtained when oxygen mole fraction was 5%. Regarding to the wastewater treatment, a significant decrease in the COD removal was obtained when the MFC performance was reduced due to the limited availability of oxygen, which indicates the significant role of the electrogenic microorganisms in the COD removal in MFC. In addition, the low availability of oxygen at the cathode leads to a lower presence of oxygen at the anode, resulting in an increase in the coulombic efficiency. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:900–907, 2015     

Associations between redox‐sensitive trace metals and microbial communities in a Proterozoic ocean analogue

Constraints on Precambrian ocean chemistry are dependent upon sediment geochemistry. However, diagenesis and metamorphism can destroy primary biosignatures, making it difficult to consider biology when interpreting geochemical data. Modern analogues for ancient ecosystems can be useful tools for identifying how sediment geochemistry records an active biosphere. The Middle Island Sinkhole (MIS) in Lake Huron is an analogue for shallow Proterozoic waters due to its low oxygen water chemistry and microbial communities that exhibit diverse metabolic functions at the sediment–water interface. This study uses sediment trace metal contents and microbial abundances in MIS sediments and an oxygenated Lake Huron control site (LH) to infer mechanisms for trace metal burial. The adsorption of trace metals to Mn‐oxyhydroxides is a critical burial pathway for metals in oxic LH sediments, but not for the MIS mat and sediments, consistent with conventional understanding of Mn cycling. Micronutrient trace metals (e.g., Zn) are associated with organic matter regardless of oxygen and sulfide availability. Although U and V are conventionally considered to be organically complexed in suboxic and anoxic conditions, U and organic covary in oxic LH sediments, and Mn‐oxyhydroxide cycling dominates V deposition in the anoxic MIS sediments. Significant correlations between Mo and organic matter across all redox regimes have major implications for our interpretations of Mo isotope systematics in the geologic record. Finally, while microbial groups vary between the sampling locales (e.g., the cyanobacteria in the MIS microbial mat are not present in LH sediments), LH and MIS ultimately have similar relationships between microbial assemblages and metal burial, making it difficult to link trace metal burial to microbial metabolisms. Together, these results indicate that bulk sediment trace metal composition does not capture microbiological processes; more robust trace metal geochemistry such as isotopes and speciation may be critical for understanding the intersections between microbiology and sediment geochemistry.     

Impacts of single‐walled carbon nanotubes on microbial community structure in activated sludge

Aims: Single‐walled carbon nanotubes (SWNTs) are likely to become increasingly widespread and yet their environmental impact is not well understood. The purpose of the current study was to evaluate the impact of SWNTs on microbial communities in a ‘sentinel’ environmental system, activated sludge batch‐scale reactors. Methods and Results: Triplicate batch reactors were exposed to SWNTs and compared to control reactors exposed to impurities associated with SWNTs. Automated ribosomal intergenic spacer analysis (ARISA) was used to assess bacterial community structure in each reactor. SWNT exposure was found to impact microbial community structure, while SWNT‐associated impurities had no effect, compared to controls. 16S rRNA gene sequence analysis indicated that dominant phylotypes detected by ARISA included members of the families Sphingomonadaceae and Cytophagacaceae and the genus Zoogloea. ARISA results indicated an adverse impact of SWNTs on the sphingomonad relative to other community members. Changes in community structure also occurred in both SWNT‐exposed and control reactors over the experimental time period and with the date on which activated sludge was obtained from a wastewater treatment facility. Conclusions: These results indicate that SWNTs differentially impact members of the activated sludge reactor bacterial community. Significance and Impact of the Study: The finding that community structure was affected by SWNTs indicates that this emerging contaminant differentially impacted members of the activated sludge bacterial community and raises the concern that SWNTs may also affect the services it provides.