@article{summers2024identification,
  title = {Identification of the bacterial community that degrades phenanthrene
  sorbed to polystyrene nanoplastics using DNA-based stable isotope
  probing},
  author = {Summers, Stephen and Bin Hudari, Md Sufian and Magill, Clayton and Henry, Theodore and Gutierrez, Tony},
  year = {2024},
  journal = {Scientific Reports},
  volume = {14},
  number = {5229},
  file = {summers2024identification.pdf},
  doi = {10.1038/s41598-024-55825-9}
}

In the Anthropocene, plastic pollution has become a new environmental biotope, the so-called plastisphere. In the oceans, nano- and micro-sized plastics are omnipresent and found in huge quantities throughout the water column and sediment, and their large surface area-to-volume ratio offers an excellent surface to which hydrophobic chemical pollutants (e.g. petrochemicals and POPs) can readily sorb to. Our understanding of the microbial communities that breakdown plastic-sorbed chemical pollutants, however, remains poor. Here, we investigated the formation of 500 nm and 1000 nm polystyrene (PS) agglomerations in natural seawater from a coastal environment, and we applied DNA-based stable isotope probing (DNA-SIP) with the 500 nm PS sorbed with isotopically-labelled phenanthrene to identify the bacterial members in the seawater community capable of degrading the hydrocarbon. Whilst we observed no significant impact of nanoplastic size on the microbial communities associated with agglomerates that formed in these experiments, these communities were, however, significantly different to those in the surrounding seawater. By DNA-SIP, we identified Arcobacteraceae, Brevundimonas, Comamonas, uncultured Comamonadaceae, Delftia, Sphingomonas and Staphylococcus, as well as the first member of the genera Acidiphilum and Pelomonas to degrade phenanthrene, and of the genera Aquabacterium, Paracoccus and Polymorphobacter to degrade a hydrocarbon. This work provides new information that feeds into our growing understanding on the fate of co-pollutants associated with nano- and microplastics in the ocean.

@article{undiandeye2024mediumchain,
  title = {Medium-chain
           carboxylates production from plant waste: kinetic study and
           effect of an enriched microbiome},
  author = {Undiandeye, Jerome and Gallegos, Daniela and Bonatelli, Maria L. and Kleinsteuber, Sabine and {Bin Hudari}, Mohammad Sufian and Abdulkadir, Nafi’u and Stinner, Walter and Sträuber, Heike},
  year = {2024},
  journal = {Biotechnology for Biofuels and Bioproducts},
  volume = {17},
  number = {1},
  pages = {79},
  file = {undiandeye2024medium-chain.pdf},
  doi = {10.1186/s13068-024-02528-y}
}

The need for addition of external electron donors such as ethanol or lactate impairs the economic viability of chain elongation (CE) processes for the production of medium-chain carboxylates (MCC). However, using feedstocks with inherent electron donors such as silages of waste biomass can improve the economics. Moreover, the use of an appropriate inoculum is critical to the overall efficiency of the CE process, as the production of a desired MCC can significantly be influenced by the presence or absence of specific microorganisms and their metabolic interactions. Beyond, it is necessary to generate data that can be used for reactor design, simulation and optimization of a given CE process. Such data can be obtained using appropriate mathematical models to predict the dynamics of the CE process.
	
In batch experiments using silages of sugar beet leaves, cassava leaves, and Elodea/wheat straw as substrates, caproate was the only MCC produced with maximum yields of 1.97, 3.48, and 0.88 g/kgVS, respectively. The MCC concentrations were accurately predicted with the modified Gompertz model. In a semi-continuous fermentation with ensiled sugar beet leaves as substrate and digestate from a biogas reactor as the sole inoculum, a prolonged lag phase of 7 days was observed for the production of MCC (C6–C8). The lag phase was significantly shortened by at least 4 days when an enriched inoculum was added to the system. With the enriched inoculum, an MCC yield of 93.67 g/kgVS and a productivity of 2.05 gMCC/L/d were achieved. Without the enriched inoculum, MCC yield and productivity were 43.30 g/kgVS and 0.95 gMCC/L/d, respectively. The higher MCC production was accompanied by higher relative abundances of Lachnospiraceae and Eubacteriaceae.
		
Ensiled waste biomass is a suitable substrate for MCC production using CE. For an enhanced production of MCC from ensiled sugar beet leaves, the use of an enriched inoculum is recommended for a fast process start and high production performance.

@article{binhudari2022effect,
  title = {Effects of temperature on microbial dehalogenation of
      organohalides: A review},
  doi = {10.1093/femsec/fiac081},
  author = {Bin Hudari, Md Sufian and Richnow, Hans H. and Vogt, Carsten and Nijenhuis, Ivonne},
  journal = {FEMS Microbiology Ecology},
  year = {2022},
  month = sep,
  pages = {fiac081},
  file = {binhudari2022effect.pdf},
  volume = {98},
  number = {9}
}

Temperature is a key factor affecting microbial activity and ecology. An increase in temperature generally increases rates of microbial processes up to a certain threshold, above which rates decline rapidly. In the subsurface, temperature of groundwater is usually stable and related to the annual average temperature at the surface. However, anthropogenic activities related to the use of the subsurface, e.g. for thermal heat management, foremost heat storage, will affect the temperature of groundwater locally. This minireview intends to summarize the current knowledge on reductive dehalogenation activities of the chlorinated ethenes, common urban groundwater contaminants, at different temperatures. This includes an overview of activity and dehalogenation extent at different temperatures in laboratory isolates and enrichment cultures, the effect of shifts in temperature in micro- and mesocosm studies as well as observed biotransformation at different natural and induced temperatures at contaminated field sites. Furthermore, we address indirect effects on biotransformation, e.g. changes in fermentation, methanogenesis, and sulfate reduction as competing or synergetic microbial processes. Finally, we address the current gaps in knowledge regarding bioremediation of chlorinated ethenes, microbial community shifts, and bottlenecks for active combination with thermal energy storage, and necessities for bioaugmentation and/or natural repopulations after exposure to high temperature.

@article{binhudari2022sulfidic,
  title = {Sulfidic acetate mineralization at {45°C} by an aquifer microbial
      community: Key players and effects of heat changes on activity and
        community structure},
  doi = {10.1111/1462-2920.15852},
  author = {Bin Hudari, Md Sufian and Richnow, Hans H. and Vogt, Carsten},
  journal = {Environmental Microbiology},
  year = {2022},
  volume = {24},
  number = {1},
  month = jan,
  pages = {370-389},
  file = {binhudari2022sulfidic.pdf}
}

High-Temperature Aquifer Thermal Energy Storage (HT-ATES) is a sustainable approach for integrating thermal energy from various sources into complex energy systems. Temperatures ≥45°C, which are relevant in impact zones of HT-ATES systems, may dramatically influence the structure and activities of indigenous aquifer microbial communities. Here, we characterized an acetate-mineralizing, sulfate-reducing microbial community derived from an aquifer and adapted to 45°C. Acetate mineralization was strongly inhibited at temperatures ≤25°C and 60°C. Prolonged incubation at 12°C and 25°C resulted in acetate mineralization recovery after 40–80 days whereas acetate was not mineralized at 60°C within 100 days. Cultures pre-grown at 45°C and inhibited for 28 days by incubation at 12°C, 25°C, or 60°C recovered quickly after changing the temperature back to 45°C. Phylotypes affiliated to the order Spirochaetales and to endospore-forming sulfate reducers of the order Clostridiales were highly abundant in microcosms being active at 45°C highlighting their key role. In summary, prolonged incubation at 45°C resulted in active microbial communities mainly consisting of organisms adapted to temperatures between the typical temperature range of mesophiles and thermophiles and being resilient to temporary heat changes.

@article{dai2022improving,
  title = {Improving the performance of bioelectrochemical sulfate removal
      by applying flow mode},
  author = {Dai, Shixiang and Harnisch, Falk and {Bin Hudari}, Md Sufian and Keller, Nina Sophie and Vogt, Carsten and Korth, Benjamin},
  journal = {Microbial Biotechnology},
  year = {2022},
  file = {dai2022improving.pdf},
  doi = {10.1111/1751-7915.14157}
}

Treatment of wastewater contaminated with high sulfate concentrations is an environmental imperative lacking a sustainable and environmental friendly technological solution. Microbial electrochemical technology (MET) represents a promising approach for sulfate reduction. In MET, a cathode is introduced as inexhaustible electron source for promoting sulfate reduction via direct or mediated electron transfer. So far, this is mainly studied in batch mode representing straightforward and easy-to-use systems, but their practical implementation seems unlikely, as treatment capacities are limited. Here, we investigated bioelectrochemical sulfate reduction in flow mode and achieved removal efficiencies (Esulfate, 89.2 ± 0.4%) being comparable to batch experiments, while sulfate removal rates (Rsulfate, 3.1 ± 0.2 mmol L−1) and Coulombic efficiencies (CE, 85.2 ± 17.7%) were significantly increased. Different temperatures and hydraulic retention times (HRT) were applied and the best performance was achieved at HRT 3.5 days and 30°C. Microbial community analysis based on amplicon sequencing demonstrated that sulfate reduction was mainly performed by prokaryotes belonging to the genera Desulfomicrobium, Desulfovibrio, and Desulfococcus, indicating that hydrogenotrophic and heterotrophic sulfate reduction occurred by utilizing cathodically produced H2 or acetate produced by homoacetogens (Acetobacterium). The advantage of flow operation for bioelectrochemical sulfate reduction is likely based on higher absolute biomass, stable pH, and selection of sulfate reducers with a higher sulfide tolerance, and improved ratio between sulfate-reducing prokaryotes and homoacetogens.

@article{binjudri2020effect,
  title = {Effect of temperature on acetate mineralization kinetics and microbial
    community composition in a hydrocarbon-affected microbial community
    during a shift from oxic to sulfidogenic conditions},
  author = {Bin Hudari, Md Sufian and Vogt, Carsten and Richnow, Hans H.},
  year = {2020},
  volume = {11},
  pages = {3183},
  doi = {10.3389/fmicb.2020.606565},
  journal = {Frontiers in Microbiology},
  file = {binhudari2020effect.pdf}
}

Aquifer thermal energy storage (ATES) allows for the seasonal storage and extraction of heat in the subsurface thus reducing reliance on fossil fuels and supporting decarbonization of the heating and cooling sector. However, the impacts of higher temperatures toward biodiversity and ecosystem services in the subsurface environment remain unclear. Here, we conducted a laboratory microcosm study comprising a hydrocarbon-degrading microbial community from a sulfidic hydrocarbon-contaminated aquifer spiked with 13 C-labeled acetate and incubated at temperatures between 12 and 80°C to evaluate (i) the extent and rates of acetate mineralization and (ii) the resultant temperature-induced shifts in the microbial community structure. We observed biphasic mineralization curves at 12, 25, 38, and 45°C, arising from immediate and fast aerobic mineralization due to an initial oxygen exposure, followed by slower mineralization at sulfidogenic conditions. At 60°C and several replicates at 45°C, acetate was only aerobically mineralized. At 80°C, no mineralization was observed within 178 days. Rates of acetate mineralization coupled to sulfate reduction at 25 and 38°C were six times faster than at 12°C. Distinct microbial communities developed in oxic and strictly anoxic phases of mineralization as well as at different temperatures. Members of the Alphaproteobacteria were dominant in the oxic mineralization phase at 12–38°C, succeeded by a more diverse community in the anoxic phase composed of Deltaproteobacteria, Clostridia, Spirochaetia, Gammaproteobacteria and Anaerolinea, with varying abundances dependent on the temperature. In the oxic phases at 45 and 60°C, phylotypes affiliated to spore-forming Bacilli developed. In conclusion, temperatures up to 38°C allowed aerobic and anaerobic acetate mineralization albeit at varying rates, while mineralization occurred mainly aerobically between 45 and 60°C; thermophilic sulfate reducers being active at temperatures > 45°C were not detected. Hence, temperature may affect dissolved organic carbon mineralization rates in ATES while the variability in the microbial community composition during the transition from micro-oxic to sulfidogenic conditions highlights the crucial role of electron acceptor availability when combining ATES with bioremediation.

@article{li2016production,
  author = {Li, Qingxin and Bin Hudari, Md Sufian and Wu, Jin Chuan},
  title = {Production of optically pure {D}-lactic acid by the combined use
    of {\textit{Weissella sp.}} {\textsc{s}26} and {\textit{Bacillus
      sp.}} {\textsc{ads}3}},
  journal = {Applied Biochemistry and Biotechnology},
  year = {2016},
  volume = {178},
  number = {2},
  pages = {285--293},
  issn = {1559-0291},
  doi = {10.1007/s12010-015-1871-0},
  file = {li2016production.pdf}
}

Optically pure D-lactic acid was produced from glucose, xylose, or starch by the combined use of Weissella sp. S26 and Bacillus sp. ADS3, two native bacterial strains isolated from Singapore environment. Weissella sp. S26 was used to ferment various sugars to lactic acid rich in D-isomer followed by sterilization of the broth and inoculation of Bacillus sp. ADS3 cells to selectively degrade acetic acid (if any) and L-lactic acid. In a simultaneous saccharification and fermentation of starch by Weissella sp. S26 in 1 L of modified MRS medium containing 50 g/L starch at 30 °C, lactic acid reached 24.2 g/L (23.6 g/L of D-isomers and 0.6 g/L of L-isomers), and acetic acid was 11.8 g/L at 37 h. The fermentation broth was sterilized at 100 °C for 20 min and cooled down to 30 °C followed by inoculation of Bacillus sp. ADS3 (10 %, v/v), and the mixture was kept at 30 °C for 115 h. Acetic acid was completely removed, and L-lactic acid was largely removed giving an optical purity of D-lactic acid as high as 99.5 %.

@article{ye2014simultaneous,
  title = {Simultaneous detoxification, saccharification and
      co-fermentation of oil palm empty fruit bunch hydrolysate for
      {L-lactic} acid production by {\textit{{B}acillus coagulans}}
      {\textsc{ji}12}},
  doi = {10.1016/j.bej.2013.12.005},
  author = {Ye, Lidan and {Bin Hudari}, {Md Sufian} and Li, Zhi and Wu, Jin Chuan},
  journal = {Biochemical Engineering J.},
  volume = {83},
  pages = {16-21},
  year = {2014},
  file = {ye2014simultaneous.pdf}
}

Bacillus coagulans JI12 was used to produce L-lactic acid from both cellulose and hemicellulose sugars of oil palm empty fruit bunch hydrolysate at 50 ◦ C without sterilization prior to fermentation. In fermentation of mixed glucose and xylose (10 g/L:100 g/L or 50 g/L:53 g/L), both sugars were simultaneously converted to L-lactic acid. B. coagulans JI12 was tolerant against up to 4 g/L of furfural and 20 g/L of acetate and able to metabolize furfural to 2-furoic acid. After acid hydrolysis, both the hemicellulosic and cellulosic fractions of oil palm empty fruit bunch were fermented to lactic acid in a simultaneous detoxification, saccharification and co-fermentation process supplemented with 25 FPU Cellic® CTec2 cellulase per g cellulose, yielding 80.6 g/L of lactic acid with a productivity of 3.4 g/L/h. Neither pre-detoxification nor separation of fermentable sugars from lignin was required. These results indicate that B. coagulans JI12 is a promising strain for L-lactic acid production from lignocellulosic biomass.   

@article{ye2013conversion,
  author = {Ye, Lidan and {Bin Hudari}, {Md Sufian} and Zhou, Xingding and Zhang, Dongxu and Li, Zhi and Wu, Jin Chuan},
  title = {Conversion of acid hydrolysate of oil palm empty fruit
      bunch to {L}-lactic acid by newly isolated {\textit{{B}acillus coagulans}}
      {\textsc{ji}}12},
  doi = {10.1007/s00253-013-4788-y},
  journal = {Appl. Microbiol. Biotechnol.},
  year = {2013},
  volume = {97},
  number = {11},
  pages = {4831--4838},
  month = jun,
  file = {ye2013conversion.pdf}
}

Cost-effective conversion of lignocellulose hydrolysate to optically pure lactic acid is commercially attractive but very challenging. Bacillus coagulans JI12 was isolated from natural environment and used to produce L-lactic acid (optical purity>99.5 %) from lignocellulose sugars and acid hydrolysate of oil palm empty fruit bunch (EFB) at 50 °C and pH 6.0 without sterilization of the medium. In fed-batch fermentation with 85 g/L initial xylose and 55 g/L xylose added after 7.5 h, 137.5 g/L lactic acid was produced with a yield of 98 % and a productivity of 4.4 g/Lh. In batch fermentation of a sugar mixture containing 8.5 % xylose, 1 % glucose, and 1 % L-arabinose, the lactic acid yield and productivity reached 98 % and 4.8 g/Lh, respectively. When EFB hydrolysate was used, 59.2 g/L of lactic acid was produced within 9.5 h at a yield of 97 % and a productivity of 6.2 g/Lh, which are the highest among those ever reported from lignocellulose hydrolysates. These results indicate that B. coagulans JI12 is a promising strain for industrial production of L-lactic acid from lignocellulose hydrolysate.

@article{ye2013highly,
  author = {Ye, Lidan and Zhou, Xingding and {Bin Hudari}, {Md Sufian} and Li, Zhi and Wu, Jin Chuan},
  title = {{Highly efficient production of {L}-lactic acid from
      xylose by newly isolated {\textit{Bacillus coagulans}}
  {\textsc{c}}106}},
  doi = {10.1016/j.biortech.2013.01.011},
  journal = {Bioresour. Technol.},
  year = {2013},
  volume = {132},
  pages = {38--44},
  month = mar,
  file = {ye2013highly.pdf}
}

Cost-effective production of optically pure lactic acid from lignocellulose sugars is commercially attractive but challenging. Bacillus coagulans C106 was isolated from environment and used to produce L-lactic acid from xylose at 50 °C and pH 6.0 in mineral salts medium containing 1–2% (w/v) of yeast extract without sterilizing the medium before fermentation. In batch fermentation with 85 g/L of xylose, lactic acid titer and productivity reached 83.6 g/L and 7.5 g/L h, respectively. When fed-batch (120 + 80 + 60 g/L) fermentation was applied, they reached 215.7 g/L and 4.0 g/L h, respectively. In both cases, the lactic acid yield and optical purity reached 95% and 99.6%, respectively. The lactic acid titer and productivity on xylose are the highest among those ever reported. Ca(OH)2 was found to be a better neutralizing agent than NaOH in terms of its giving higher lactic acid titer (1.2-fold) and productivity (1.8-fold) under the same conditions.

@mastersthesis{mscthesis,
  title = {Investigating Hydrocarbon-Degrading Bacteria Associated with
  Marine Phytoplankton using DNA-Based Stable Isotope Probing},
  author = {{Bin Hudari}, Mohammad Sufian},
  school = {Heriot-Watt University},
  year = {2017},
  file = {mscthesis.pdf}
}

Marine hydrocarbon-degrading bacteria play an important role in the biodegradation of oil hydrocarbon pollutants in the marine environment. Previous studies have successfully isolated hydrocarbon-degrading bacteria found associated with laboratory cultures of ma- rine phytoplankton. A recent study has shown a dramatic succession of diatom-associated bacterial community, defined by a transition from a short-lived bloom of Methylophaga to several groups including hydrocarbonoclastic bacteria on marine diatom Skeletonema costa- tum, in response to crude oil enrichment. However, little is still known about the temporal dynamics of the bacterial symbionts associated with marine phytoplankton and whether Methylophaga are directly involved in the degradation of hydrocarbons. In this investiga- tion, DNA-based stable isotope probing (DNA-SIP), which is a valuable tool that allows to link the phylogenetic identity with a specific metabolic function, was employed to identify hydrocarbon-degrading living associated with a laboratory culture of the cosmopolitan marine diatom Skeletonema costatum (CCAP 1077/1C). For this, the diatom was enriched with uniformly 13C-labelled n-hexadecane as the sole carbon source in a seawater medium. Denaturing gradient gel electrophoresis (DGGE) analysis of ‘heavy’ DNA at day 8 from the DNA-SIP incubation revealed several distinct bands, that were either not present or whose intensity was less in the ‘light’ DNA. DGGE analysis of the fractions suggests the presence of several species of hexadecane-degrading bacteria that are living associated with the diatom Skeletonema costatum. Future work will explore the phylogenetic identity of the 13C-enriched bacterial community comprising the heavy DNA by barcoded-amplicon Illumina MiSeq sequencing. This work demonstrates the value of DNA-SIP as a sophisti- cated molecular tool in microbial ecology to identify novel taxa associated with marine phytoplankton and that possesses the ability to perform a target metabolic function – in this case the degradation of hydrocarbons.