Microbial Characterization and Biosolids Processing Technology

Facebook’s algorithm for feeding me stories is insanely on-target. No more than a few minutes after Facebook presented me with the new posting from the University of California San Diego of a one-hour lecture on aging and the gut microbiome, I was transfixed to the screen. And, it got me into action, i.e. spending money, which well-targeted Facebook feeds are intended to do.

The video, supported by UDSD’s Stein Institute for Research on Aging, is Microbiomes and Aging with Rob Knight - Research on Aging.  The outcome is that I am now a “citizen scientist” with the American Gut, a project co-founded by Rob Knight.  I signed up myself and my wife (or my cat, Alice, if the wife, Kathy, balks) to participate in an international survey of gut microflora, all for a simple contribution of $100 each. I also receive the necessary sampling kit and questionnaire, along with apre-paid return packaging, and a cool tee-shirt.  According to the website, I am contributor number 8,911, which you can guess is an amazing start ( American Gut Project Crowdfunds $1 Million to Study the Human Microbiome.)  I was so excited with my contribution that, for at least a few moments, I entertained the thought of a quick trip to San Diego to participate in Knight’s Center for Microbiome Innovation Research Summit on Wednesday March 15th, 2017, at UC San Diego. The snowstorm kept me home.

Knight’s webcast from UCSD included some juicy tidbits of information, so to speak. He asserts that the crashing cost of DNA characterization will transform scientists’ ability to understand the role of human microflora in our health. His research, for instance, has drawn close associations between patterns of microbial communities and physical manifestations of metabolic disease syndrome (Gut microbiome and metabolic diseases) and of auto-immune diseases (House dust exposure mediates gut microbiome Lactobacillus enrichment and airway immune defense against allergens and virus infection). Knight showed a slide of a toddler in toilet training gazing into a cell phone, but he described a fascinating future of a toilet sensor scanning for health status changes and disease organisms during the daily visit. Knight is also a popularizer of science (check out his lecture onTEDTalk and his book on Amazon), and you can take his online Coursera class Gut Check: Exploring Your Microbiome, in which he includes a web-interview with food journalist, Michael Pollen, author of Omnivore’s Dilemma: A Natural History of Four Meals, whom he had enrolled in being an early participant (See Lecture 51).  Can you doubt but that we are on the verge of improving bodily health by intentionally managing gut microbiota?

I was thrilled to learn that Knight is not just into the gut. He is the co-founder, too, of the Earth Microbiome Project, EMP.  According to Wikipedia: “The primary goal of EMP is to survey microbial composition in many environments across the planet, across time as well as space, using a standard set of protocols.”  The EMP is already spawning fascinating research, such as examining the role of microbiomes in the unique nature of 5 different Cannabis varieties or in the "organoleptic properties" that imbue wine with a particular "terroir."  Wine and pot may be intriguing topics driving new EMP research, but I wondered how even more exciting EMP would be with studies of biosolids. I think this could really happen, as one of the founding EMP leaders, Jack A. Gilbert, a Chicago-based scientist, is releasing his Dirt is Good book in June—my kind of researcher!

You see, I already had this great idea.  With prices of microbiota and microbiome research plummeting, it is not too early to begin planning for the “American Biosolids Project.” This would, after all, be sort of an obvious and useful melding of both the AGP and the EMP, a conjoining of two great ideas!

This thought so excited me that I contacted the AGP/EMP team to see if I could round up a few biosolids cake samples from around the U.S. to send for microbiota analysis. I am waiting on an answer. I will let you all know if I get a “green light.” I will then put out the call to you all.

I knew at least one other person would be as thrilled as me with the concept of the American Biosolids Project. That is Virginia Tech PhD candidate Josh Mah, who has been doing metagenomic analyses of municipal anaerobic digesters, particularly DC Water’s.

 I called Josh and to my delight learned that he had attended several events at which Dr. Knight was speaker or moderator, including a symposium by the Center for Microbiome Innovation. I learned, too, that Mah had suggested anaerobic digesters as a part of the EMP and American Gut project toolbox. No way!!! And, Rob Knight seemed interested! Again, no way!!!

Josh reminded me that this research area is not terribly new.  I had written in previous essays about the work of Jordan Peccia’s Environmental Biotech Lab at Yale, with students Kyle Bibby and Emily Viau, on the bacterial pathogens and viruses sequenced in a variety of biosolids samples. But I hadn’t embraced the vision that we might actively manage treatment processes and quality control by monitoring the biosolids microbiome.

I delved into Google Scholar.  From across the globe, research teams are now working on basic aspects of anaerobic digester microbial communities. In Using a combination of binning strategies and taxonomic approaches to unravel the anaerobic digestion microbiome the research team worked to combine analytical approaches that accomplish the  “computational effort needed for the taxonomic assignment of hundreds of new microbial genomes.” Another team discovered a lot of “community diversity” differences between different digesters, Predictive functional profiling using marker gene sequences and community diversity analyses of microbes in full-scale anaerobic sludge digesters . Another examined how digesters alter the microbial communities in the sludge feedstock, observing that a significant part of input “volatile solids” (about 82%) are microbes that are replaced as VS with microbial biomass from communities within the digester (Evaluating digestion efficiency in full-scale anaerobic digesters by identifying active microbial populations through the lens of microbial activity.)  In Deeper insight into the structure of the anaerobic digestion microbial community; the biogas microbiome database is expanded with 157 new genomes, a research team concluded that “this analysis led to the identification of a subset of common microbes that could be considered as the core essential group in biogas production.”  The intention is to optimize for biogas production.

While biogas is well and good, my enthusiasm with microbes is tied to the American Gut idea that we can learn useful lessons for achieving "high quality biosolids" from a large population study of microbiomes. So, I needed to check into a range of other biosolids processes.  When I shifted away from anaerobic digestion over to aerobic digestion, I could find no research reports. In fact, Google Scholar insisted that I wanted results for anaerobic digestion, not aerobic digestion, and auto corrected my search.

I jumped to composting and found only a few promising entries on metagenomics. The journal article Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition enthusiastically reports: “These data underline the pivotal role of thermophilic Actinobacteria in lignocellulose biodegradation processes in the compost habitat.”  A group from Brazil, looking at the composting of “zoo doo” in Sao Paulo, reported in Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomic, that: “Moreover, our sequencing data allowed near-complete genome reconstruction of five bacterial species previously found in biomass-degrading environments and of a novel biodegrading bacterial species, likely a new genus in the order Bacillales. The data and analyses provided are a rich source for additional investigations of thermophilic composting microbiology.”  Composting is extraordinarily capable of transforming organic matter, so I believe this research area will be “fertile” in the future.

We are still in the infancy of this research. The American Gut project was not conceivable at the time the Human Microbiome Project was initiated in 2008, as a $115 million, 6-year effort. So, we understandably find inconceivable the notion that we have a future in which our water reclamation facilities and the biosolids products are continually monitored and tracked for stability and microbial safety using these tools. 

One tantalizing evidence of potential value to our profession of metagenomic research is in odor control. Josh brought to my attention this recent journal article: Chasing the elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious methyl-reducing methanogen.  One implication of this study is that “These findings reveal a remarkably unique methanogen /`Candidatus Methanofastidiosum methylthiophilus/' as the first insight into the sixth class of methanogens /`Candidatus Methanofastidiosa/'," where these organisms are “sulfur eaters,” which many mean they metabolize biosolids odorants. Perhaps these are the organisms inactivated by centrifuges, causing a sharp rise in odor intensity, and whose populations need to rebound over several weeks of storage.  As another example, when we are working with an aerobic process, whether digestion or composting, we might discover additives for accelerating processes and reducing costs. The report,  Assessment of bacterial diversity during composting of agricultural byproducts,  found  “some novel bacterial isolates like Kocuria, Microbacterium, Acidovorax and Comamonas first time from agro-byproducts compost… potential compost inoculants....” 

Science has given us powerful new tools for microbial characterization of environmental samples. Biosolids is an amazing cross over between the American Gut and the Environmental Microbiome Project spheres. We cannot begin to imagine the ramifications of embracing these tools for the design of new processing technology and for the characterization of biosolids quality and its performance in the land application. But our lack of imagination should not stop us from committing to moving forward with the work. Someday we may look back and realize that our future had been defined by the American Biosolids Project