@article{haq_malik_khan_weaver_wang_khan_khan_shah_ahmed_jamal_et al._2023, title={Effect of removal of inhibitors on microbial communities and biogas yield of <i>Jatropha curcas</i> seeds during continuous anaerobic digestion}, volume={426}, ISSN={["1879-1786"]}, url={https://doi.org/10.1016/j.jclepro.2023.139154}, DOI={10.1016/j.jclepro.2023.139154}, abstractNote={Jatropha curcas seeds, as an abundant lignocellulosic biomass, offer a highly promising and ideal alternative for producing energy in the form of methane. Use of J. curcas seeds has the potential to significantly bolster the biofuel sector, fostering a more sustainable circular economy. In the current study, different fractions of processed J. curcas seeds were investigated for biogas production. J. curcas seed pressed cake, a by-product of biodiesel production, was subjected to methanolic extraction. The remaining solids, referred to as methanolic residues, yielded more biogas in batch experiments than pressed cake and residues from aqueous and n-hexane extractions. The compounds extracted with methanol inhibited hydrolysis and reduced biogas production by 35.5% compared to the same setup without extracts. In continuous reactors fed with methanolic residues, the highest biogas yield occurred at an organic loading rate (OLR) of 1 g VS L−1 day−1 and a hydraulic retention time (HRT) of 20 days. The relative abundance of acetogenic bacteria was higher in reactors fed with methanolic residues than in those fed with seed pressed cake, seed oil, and whole seed. Jatropha seed oil and whole seed did not inhibit methanogens. A higher relative abundance of methanogenic communities was observed in all reactors at HRT of 20 days compared to those at HRTs at 15 and 10 days. These findings can be used to increase biogas production during anaerobic digestion of J. curcas seed components and suggests a zero-waste biorefinery production route for value added compounds derived from the removal of biogas-inhibiting components.}, journal={JOURNAL OF CLEANER PRODUCTION}, publisher={Elsevier BV}, author={Haq, Abdul and Malik, Ayesha and Khan, Alam and Weaver, Joseph E. and Wang, Ling and Khan, Haji and Khan, Samiullah and Shah, Aamer Ali and Ahmed, Safia and Jamal, Asif and et al.}, year={2023}, month={Nov} }
 @article{weaver_2023, title={Quantifying drift-selection balance using an agent-based biofilm model of identical heterotrophs under low-nutrient conditions}, url={https://doi.org/10.1098/rsfs.2023.0010}, DOI={10.1098/rsfs.2023.0010}, abstractNote={Both deterministic and stochastic forces shape biofilm communities, but the balance between those forces is variable. Quantifying the balance is both desirable and challenging. For example, drift-driven failure, a stochastic force, can be thought of as an organism experiencing ‘bad luck’ and manipulating ‘luck’ as a factor in real-world systems is difficult. We used an agent-based model to manipulate luck by controlling seed cevalues governing random number generation. We determined which organism among identical competitors experienced the greatest drift-driven failure, gave it a deterministic growth advantage and re-ran the simulation with the same seed. This enabled quantifying the growth advantage required to overcome drift, e.g. a 50% chance to thrive may require a 10–20% improved growth rate. Further, we found that crowding intensity affected that balance. At moderate spacings, there were wide ranges where neither drift nor selection dominated. Those ranges shrank at extreme spacings; close and loose crowding, respectively, favoured drift and selection. We explain how these results may partially illuminate two conundrums: the fact that a stably operating wastewater treatment plant's microbial community can vary greatly over time and the difference between equivalent and total community size in neutral community assembly models.}, journal={Interface Focus}, author={Weaver, Joseph Earl}, year={2023}, month={Aug} }
 @article{weaver_2022, title={Quantifying Drift-Fitness Balance Using an Agent-Based Biofilm Model of Identical Heterotrophs Under Low Nutrient Conditions}, url={https://doi.org/10.1101/2022.12.08.519628}, DOI={10.1101/2022.12.08.519628}, abstractNote={AbstractBoth deterministic and stochastic forces shape biofilm communities, but the balance between those forces is variable. Quantifying the balance is both desirable and challenging. For example, negative drift selection, a stochastic force, can be thought of as an organism experiencing ‘bad luck’ and manipulating ‘luck’ as a factor in real world systems is difficult. We used an agent-based model to manipulate luck by controlling seed values governing random number generation. We determined which organism among identical competitors experienced the greatest negative drift selection, gave it a deterministic growth advantage, and re-ran the simulation with the same seed. This enabled quantifying the growth advantage required to overcome drift,e.g., a 50% chance to thrive may require a 10-20% improved growth rate. Further, we found that crowding intensity affected that balance. At moderate spacings, there were wide ranges where neither drift nor growth dominated. Those ranges shrank at extreme spacings; close and loose crowding respectively favoured drift and growth. We explain how these results may partially illuminate two conundrums: the difference between taxa and functional stability in wastewater treatment plans and the difference between equivalent and total community size in neutral community assembly models.}, author={Weaver, Joseph Earl}, year={2022}, month={Dec} }
 @article{wu_ning_zhang_li_zhang_shan_zhang_brown_li_van nostrand_et al._2019, title={Global diversity and biogeography of bacterial communities in wastewater treatment plants}, volume={4}, ISSN={2058-5276}, url={http://dx.doi.org/10.1038/s41564-019-0426-5}, DOI={10.1038/s41564-019-0426-5}, abstractNote={Microorganisms in wastewater treatment plants (WWTPs) are essential for water purification to protect public and environmental health. However, the diversity of microorganisms and the factors that control it are poorly understood. Using a systematic global-sampling effort, we analysed the 16S ribosomal RNA gene sequences from ~1,200 activated sludge samples taken from 269 WWTPs in 23 countries on 6 continents. Our analyses revealed that the global activated sludge bacterial communities contain ~1 billion bacterial phylotypes with a Poisson lognormal diversity distribution. Despite this high diversity, activated sludge has a small, global core bacterial community (n = 28 operational taxonomic units) that is strongly linked to activated sludge performance. Meta-analyses with global datasets associate the activated sludge microbiomes most closely to freshwater populations. In contrast to macroorganism diversity, activated sludge bacterial communities show no latitudinal gradient. Furthermore, their spatial turnover is scale-dependent and appears to be largely driven by stochastic processes (dispersal and drift), although deterministic factors (temperature and organic input) are also important. Our findings enhance our mechanistic understanding of the global diversity and biogeography of activated sludge bacterial communities within a theoretical ecology framework and have important implications for microbial ecology and wastewater treatment processes.}, number={7}, journal={Nature Microbiology}, publisher={Springer Science and Business Media LLC}, author={Wu, Linwei and Ning, Daliang and Zhang, Bing and Li, Yong and Zhang, Ping and Shan, Xiaoyu and Zhang, Qiuting and Brown, Mathew and Li, Zhenxin and Van Nostrand, Joy D. and et al.}, year={2019}, month={May}, pages={1183–1195} }
 @article{weaver_williams_ducoste_de los reyes_2019, title={Measuring the Shape and Size of Activated Sludge Particles Immobilized in Agar with an Open Source Software Pipeline}, volume={1}, ISSN={1940-087X}, url={http://dx.doi.org/10.3791/58963}, DOI={10.3791/58963}, abstractNote={Experimental bioreactors, such as those treating wastewater, contain particles whose size and shape are important parameters. For example, the size and shape of activated sludge flocs can indicate the conditions at the microscale, and also directly affect how well the sludge settles in a clarifier. Particle size and shape are both misleadingly 'simple' measurements. Many subtle issues, often unaddressed in informal protocols, can arise when sampling, imaging, and analyzing particles. Sampling methods may be biased or not provide enough statistical power. The samples themselves may be poorly preserved or undergo alteration during immobilization. Images may not be of sufficient quality; overlapping particles, depth of field, magnification level, and various noise can all produce poor results. Poorly specified analysis can introduce bias, such as that produced by manual image thresholding and segmentation. Affordability and throughput are desirable alongside reproducibility. An affordable, high throughput method can enable more frequent particle measurement, producing many images containing thousands of particles. A method that uses inexpensive reagents, a common dissecting microscope, and freely-available open source analysis software allows repeatable, accessible, reproducible, and partially-automated experimental results. Further, the product of such a method can be well-formatted, well-defined, and easily understood by data analysis software, easing both within-lab analyses and data sharing between labs. We present a protocol that details the steps needed to produce such a product, including: sampling, sample preparation and immobilization in agar, digital image acquisition, digital image analysis, and examples of experiment-specific figure generation from the analysis results. We have also included an open-source data analysis pipeline to support this protocol.}, number={143}, journal={Journal of Visualized Experiments}, publisher={MyJove Corporation}, author={Weaver, Joseph E. and Williams, Jon C. and Ducoste, Joel J. and de los Reyes, Francis L., III}, year={2019}, month={Jan} }
 @inbook{weaver_wang_de los reyes_barlaz_2019, title={Systems and Methods for Studying Microbial Processes and Communities in Landfills}, ISBN={9783030107758 9783030107772}, ISSN={2366-3324 2366-3332}, url={http://dx.doi.org/10.1007/978-3-030-10777-2_5}, DOI={10.1007/978-3-030-10777-2_5}, abstractNote={The objective of this chapter is to review research on the microbiology of landfills. This chapter focuses on anaerobic reactions that dominate waste decomposition in engineered landfills and begins with a brief description of the major components of a sanitary landfill followed by a discussion of MSW (municipal solid waste) composition. The processes by which cellulosic substrates are converted to CH4 and CO2 are described. Systems for studying landfill processes (including testing setups and sampling) are then discussed, followed by traditional and molecular methods that have been used to investigate the microbial ecology of landfills.}, booktitle={Advances in Environmental Microbiology}, publisher={Springer International Publishing}, author={Weaver, Joseph E. and Wang, Ling and de los Reyes, Francis L. and Barlaz, Morton A.}, year={2019}, pages={129–150} }
 @article{weaver_hong_ducoste_de los reyes_2018, title={Controlling aerobic biological floc size using Couette-Taylor Bioreactors}, volume={147}, ISSN={0043-1354}, url={http://dx.doi.org/10.1016/j.watres.2018.09.060}, DOI={10.1016/j.watres.2018.09.060}, abstractNote={Biological floc size is an important reactor microenvironment parameter that is often not experimentally controlled due to a lack of suitable methods. Here, we introduce the Couette-Taylor bioreactor (CTB) as an improved tool for controlling biological floc size, specifically as compared with bubble-column sequencing batch reactors (SBRs). A CTB consists of two concentric walls, either of which may be rotated to induce fluid motion. The induced flow produces hydrodynamic shear which is more uniform than that produced through aeration in SBRs. Because hydrodynamic shear is a major parameter controlling floc size, we hypothesized the ability to better control shear rates within a CTB would enable better-controlled floc sizes. To test this hypothesis, we measured the particle size distributions of activated sludge flocs from CTBs with either inner (iCTB) or outer (oCTB) rotating walls as well as SBRs with varying height to diameter ratios (0.5, 1.1, and 9.4). The rotation speed of the CTBs and aeration rate of the SBRs were varied to produce predicted mean shear rates from 25 to 250 s−1. Further, the shear rate distributions for each experiment were estimated using computational fluid dynamics (CFD). In all SBR experiments, the floc distributions did not significantly vary with shear rate or geometry, likely because shear rates (estimated by CFD) differed much less than originally predicted by theory. In the CTB experiments, the mean particle size decreased proportionally with increased hydrodynamic shear, and iCTBs produced particle size distributions with smaller coefficients of variation than oCTBs (0.3 vs. 0.5–0.7, respectively).}, journal={Water Research}, publisher={Elsevier BV}, author={Weaver, Joseph E. and Hong, Hyunsuk and Ducoste, Joel J. and de los Reyes, Francis L., III}, year={2018}, month={Dec}, pages={177–183} }
 @inproceedings{weaver_ducoste_de los reyes iii_2016, title={Fluid shear variation potentially plays a role in aerobic granular sludge formation}, volume={2016}, DOI={10.2175/193864716819706734}, number={11}, booktitle={Proceedings of the Water Environment Federation, WEFTEC 2016}, author={Weaver, JE and Ducoste, JJ and de los Reyes III, FL}, year={2016}, pages={5737–5744} }
 @article{de los reyes_weaver_wang_2015, title={A methodological framework for linking bioreactor function to microbial communities and environmental conditions}, volume={33}, ISSN={0958-1669}, url={http://dx.doi.org/10.1016/j.copbio.2015.02.002}, DOI={10.1016/j.copbio.2015.02.002}, abstractNote={In the continuing quest to relate microbial communities in bioreactors to function and environmental and operational conditions, engineers and biotechnologists have adopted the latest molecular and 'omic methods. Despite the large amounts of data generated, gaining mechanistic insights and using the data for predictive and practical purposes is still a huge challenge. We present a methodological framework that can guide experimental design, and discuss specific issues that can affect how researchers generate and use data to elucidate the relationships. We also identify, in general terms, bioreactor research opportunities that appear promising.}, journal={Current Opinion in Biotechnology}, publisher={Elsevier BV}, author={de los Reyes, Francis L, III and Weaver, Joseph E and Wang, Ling}, year={2015}, month={Jun}, pages={112–118} }
 @phdthesis{weaver, place={Raleigh, NC}, title={Effect of Inoculum Source on the Rate and Extent of Anaerobic Biodegradation}, school={North Carolina State University}, author={Weaver, J.E.} }