First first-authorship paper accepted for Olivia Choi from the Kamath Lab!

Olivia Choi, a doctoral candidate in the Kamath lab at the University of Maine, has had her first scientific paper accepted for which she is the first author – a position indicative of the amount of work and organization that she put into developing this work and wrangling the large research team involved. Olivia’s graduate work is winding down as she concentrates on writing up papers and her dissertation, and she is planning on defending her PhD and looking for a postdoc in 2022 in wild animal microbiomes and ecology.

Olivia brought this 16S rRNA dataset to use in my AVS590 data analysis class back in spring 2020, of bacterial communities in different locations on birds of different species, which had been sampled as part of her dissertation work on bird migration and range changes, microbial carriage, and risk of transmission of microbes to other animals. I mentored her through analysis and preliminary manuscript writing as part of that course. The research team generously invited me to join the author team, and I continued to provide mentorship as Olivia worked through the complex task of melding various types of microbiology data.

Choi, O., Corl, A., Lublin, A., Ishaq, S.L., Charter, M., Pekarsky, S., Thie, N., Tsalyuk, M., Turmejan, S., Wolfenden, A., Bowie, R.C.K., Nathan, R., Getz, W.M., Kamath, P.L. 2021. High-throughput sequencing for examining Salmonella prevalence and pathogen – microbiota relationships in barn swallows. Frontiers in Ecology and Evolution 9:681.


Studies in both humans and model organisms suggest that the microbiome may play a significant role in host health, including digestion and immune function. Microbiota can offer protection from exogenous pathogens through colonization resistance, but microbial dysbiosis in the gastrointestinal tract can decrease resistance and is associated with pathogenesis. Little is known about the effects of potential pathogens, such as Salmonella, on the microbiome in wildlife, which are known to play an important role in disease transmission. Recent studies have expanded the traditional use of 16S rRNA gene amplicon data from high-level characterization of host-associated microbial communities (i.e., the microbiome) to detection of specific bacteria. Few studies, however, have evaluated the ability of high-throughput 16S rRNA gene sequencing data to detect potential bacterial pathogens in comparison with laboratory culture-based methods. To address this knowledge gap, we evaluated the utility of 16S rRNA gene sequencing for potential pathogen detection and explored the relationship between potential pathogens and microbiota. First, we compared the detection of Salmonella spp. in barn swallows (Hirundo rustica) using 16S rRNA data with standard culture techniques. Second, we examined the prevalence of Salmonella using 16S rRNA data and examined the relationship between Salmonella presence or absence and individual host factors. Lastly, we evaluated host-associated bacterial diversity and community composition in Salmonella present versus absent birds. Out of 108 samples, we detected Salmonella in 6 (5.6%), 25 (23.1%), and 3 (2.8%) samples based on culture, unrarefied 16S rRNA gene sequencing data, and both techniques, respectively. In addition, we found that Salmonella presence and absence differed between birds based on migratory status and weight and that bacterial community composition and diversity differed between Salmonella present versus absent birds, with eleven bacterial taxa differentially abundant between the two groups. The results of this study highlight the value of high-throughput 16S rRNA gene sequencing data for bacterial pathogen detection and for examining relationships between potential pathogens and host-associated microbial communities. Further, this study emphasizes an approach using 16S rRNA gene sequencing data for simultaneously monitoring multiple pathogens in wild avian reservoirs, which is important for prediction and mitigation of disease spillover into livestock and humans. 

This work was presented at a recent scientific conference:

Choi*, O.N., Corl, A., Wolfenden, A., Lublin, A., Ishaq, S.L., Turjeman, S., Getz, W.M., Nathan, R., Bowie, R.C.K., Kamath, P.L. “High-throughput sequencing for examining Salmonella prevalence and pathogen -microbiota relationships in barn swallows.”  69th Annual – 14th Biennial Joint Conference of the Wildlife Disease Association & European Wildlife Disease Association. (virtual). Aug 31 – Sept 2, 2021.

Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice

The Microbes and Social Equity Working Group is delighted to make its published debut, with this collaboratively-written perspective piece introducing ourselves and our goals. You can read about us here.

This piece also debuts the special series we are curating in partnership with the scientific journal mSystems; “Special Series: Social Equity as a Means of Resolving Disparities in Microbial Exposure“. Over the next few months to a year, we will be adding additional peer-reviewed, cutting edge research, review, concept, and perspective pieces from researchers around the globe on a myriad of topics which center around social inequity and microbial exposures.

Ishaq, S.L., Parada, F.J., Wolf, P.G., Bonilla, C.Y., Carney, M.A., Benezra, A., Wissel, E., Friedman, M., DeAngelis, K.M., Robinson, J.M., Fahimipour, A.K., Manus, M.B., Grieneisen, L., Dietz, L.G., Pathak, A., Chauhan, A., Kuthyar, S., Stewart, J.D., Dasari, M.R., Nonnamaker, E., Choudoir, M., Horve, P.F., Zimmerman, N.B., Kozik, A.J., Darling, K.W., Romero-Olivares, A.L., Hariharan, J., Farmer, N., Maki, K.A., Collier, J.L., O’Doherty, K., Letourneau, J., Kline, J., Moses, P.L., Morar, N. 2021. Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice. mSystems 6:4.

Interview with WeTalkScience: animal microbiome

A few weeks ago, I sat down with Sheba A-J, one of the producers of the WeTalkScience podcast, to talk about one of my recent publications in the research journal iScience, at which Sheba is also an editor. Listen to find out how lobsters are like humans, how I got involved on a project working with ants and nematodes, and how you can help make science a more welcoming place.

The full publication is:

Ishaq, S.L., A. Hotopp, S. Silverbrand, J.E. Dumont, A. Michaud, J. MacRae, S. P. Stock, E. Groden. 2021. Bacterial transfer from Pristionchus entomophagus nematodes to the invasive ant Myrmica rubra and the potential for colony mortality in coastal Maine. iScience 24(6):102663. Article.

Paper published on animal feed and rumen bacteria

I’m delighted to announce that a paper was published on the effect of a dietary additive on the rumen and fecal bacterial communities in dairy cattle, in the journal Animal: The International Journal of Animal Biosciences!

A lot of factors can be manipulated to help get the most out of one’s diet, including the source and processing method of the ingredients – in most cases in livestock feed: plants. Growing plants for animal feed can be expensive, and often nutrients in plants become more available to the animal after the plant has been processed/broken down in some way. This sometimes allows for food byproducts to be reused for animal feed, and one common example is used brewers’ grains. Once the grains have been fermented to produce alcohol, the simple sugars have been used up but a lot of the complex sugar carbohydrates – in other words: fiber – are left over. Ruminants don’t need simple sugars, but they do need a lot of fiber, and brewers’ grains have been investigated for their usefulness for animal nutrition because they are a cheap, readily-available, and common source of fiber, as well as protein.

The original experiment for this work took place several years ago, and involved an animal feeding trial which added reduced-fat distillers’ grains with solubles into dairy cattle feed. The research team found no negatives effect on milk production or animal health, and that work was previously published. To add to that project, the original research team wanted to know if the diet would drastically change the bacterial community living in the rumen, which would have implications for feed digestion and animal health.

A collaborator of mine donated the cow microbial community DNA data to my AVS 590 special topics in DNA Sequencing Data Analysis course in spring 2020 (now formally registered as AVS 454/554). I worked with UMaine graduate students Adwoa Dankwa and Usha Humagain over the semester to train them in coding and develop the manuscript. The diet only had minimal effects on the bacterial community profiles, which in this case is a good finding – we want to be able to feed a cheap, nutritional source like distillers’ grains without harming the cow or its microbes.

Dankwa, A.S., U. Humagain, S.L. Ishaq, C.J. Yeoman, S. Clark , D.C. Beitz, and E. D. Testroet. 2021. Determination of the microbial community in the rumen and fecal matter of lactating dairy cows fed on reduced-fat dried distillers grains with solubles. Animal 15(7):100281.


Reduced-fat dried distillers’ grains with solubles (RF-DDGS) is a co-product of ethanol production and contains less fat than traditional distillers’ grains. The fat in corn is ~ 91% unsaturated, and it is toxic to rumen microorganisms so it could influence the composition of the rumen microbiome. It has been demonstrated that RF-DDGS is a suitable ration ingredient to support the high-producing dairy cow, and this feedstuff is a promising alternative protein source for lactating dairy cows. The current study aims to better understand the effect of RF-DDGS on the rumen and fecal bacterial composition in lactating dairy cows. Thirty-six multiparous (2 or 3), mid-lactation Holstein cows (BW = 680 ± 11 kg; 106 ± 27 DIM) were randomly assigned to two groups which were fed a control diet made up of corn, corn silage, and alfalfa hay supplemented with expeller soybean meal or with added RF-DDGS (20% of the dry matter (DM)) containing approximately 6.0% fat. Whole rumen contents (rumen fluid and digesta; esophageal tubing method) and feces (free catch method) were collected on day 35 of the experimental period, after the 14-d acclimation period. Rumen contents and feces from each cow were used for DNA extraction. The bacterial community composition in rumen and fecal samples was assessed via the 16S rRNA gene by using the Illumina MiSeq sequencing platform. Bacteroidetes, Actinobacteria, and Firmicutes were the most abundant phyla in rumen contents. The fecal microbiota was dominated by the phyla Firmicutes and Bacteroidetes, as well as Actinobacteria and Chloroflexi. RF-DGGS increased bacterial richness, evenness, and Shannon diversity in both rumen and fecal samples and was associated with several taxa that had different abundance in treatment versus control comparisons.  The RF-DGGS, however, did not significantly alter the bacterial community in the rumen or feces. In general, these findings demonstrated that dietary inclusion of RF-DDGS did not impose any serious short-term (within 30 days) health or production consequences, as would be expected. With this study, we present further evidence that inclusion of 20% (DM basis) RF-DDGS in the diet of lactating dairy cows can be done without consequence on the microbiome of the rumen.


Reduced-fat dried distillers’ grains with solubles is a quality, economical, and readily available protein source demonstrated to support the protein needs of high-producing dairy cows. In this study, the rumen and fecal bacterial communities of lactating dairy cows were not significantly influenced by 20% (dry matter basis) reduced-fat dried distillers’ grains with solubles and did not impose serious short-term (within 30 days) health or production consequences. This diet could potentially be introduced into Total Mixed Ration feeding of dairy cattle given the fact that it is readily available and relatively economical.

Illustrated image of a cross section of the ground. A light brown ant is pictured in the ground along with a microbe. Text to the left of the image reads, "Can a necromenic nematode serve as a biological Trojan horse for an invasive ant?". The names of six professors are listed below the text and image at the bottom left. In the bottom right corner, text reads, "The University of Maine" with "The University of Arizona" below it.

Paper published on bacterial transfer in insects and possible ecological impacts.

A collaborative paper on bacterial transfer in insects and the possible ecological impacts of that in the wild has been published in iScience! This work began a decade ago in the labs of Dr. Ellie Groden, recently retired Professor of Entomology in the School of Biology and Ecology at the University of Maine, and later Dr. Patricia Stock, a Professor in the School of Animal and Comparative Biomedical Sciences at the University of Arizona, who were investigating colony collapse of European fire ants (Myrmica rubra) which are invasive to Maine. The ants have a nasty bite, and can dramatically disturb the local plant and insect wildlife in coastal Maine.

Slide from Ishaq et al. Entomology 2020 presentation

When these invasive ant colonies collapsed, Drs. Groden and Stock wanted to find out why, as a possible means of developing a biological control strategy. It was thought that particular nematodes would ingest soil bacteria, and transfer it to ants once the worms invaded ant tissues to complete parts of their life cycle. This particular worm infection doesn’t kill the ants, but perhaps the soil bacteria were. Ants were collected from different colony sites, and investigations on the nematode worms inhabiting the ants were conducted.

Slide from Ishaq et al. Entomology 2020 presentation

Most of the work for this project was completed several years ago, with the exception of DNA sequencing data from a bacterial transfer experiment. I was added to the project by my collaborator at UMaine, Dr. Jean MacRae, an Associate Professor in the Department of Civil and Environmental Engineering who introduced me to the research team and shared the 16S rRNA dataset to use in my AVS 590 data analysis class in spring 2020. That semester was when the pandemic hit, and forced the course to move to remote-only instruction in March. UMaine graduate students Alice Hotopp and Sam Silverbrand were taking the class and learning 16S analysis on this dataset, and I mentored them through the analysis all the way to manuscript writing despite the incredible challenges that spring threw our way.

At the completion of the course, we shared the draft manuscript with the rest of the research team, who mentioned that several undergraduate honor’s theses had been written about the earlier experiment, but never published in a scientific journal. The team spent summer 2020 combining the three papers into one massive draft. The pandemic slowed down manuscript review, understandably, but I’m pleased to say that it was accepted for publication! In addition, this collaboration has led to further collaborations in the Ishaq Lab, several presentations (listed below), and is Sam’s first scientific publication, congrats Sam!!

Related Presentations

Alice Hotopp, A., Samantha Silverbrand, Suzanne L. Ishaq, Jean MacRae, S. Patricia Stock, Eleanor Groden. “Can a necromenic nematode serve as a biological Trojan horse for an invasive ant?Ecological Society of America 2021 (virtual). Aug 2-6, 2021 (accepted poster).

Ishaq*, S.L., Hotopp, A., Silverbrand, S.,   MacRae, J.,  Stock, S.P.,  Groden, E. “Can a necromenic nematode serve as a biological Trojan horse for an invasive ant?” Entomological Society of America 2020 (virtual). Nov 15-25, 2020. (invited talk)

Illustrated image of a cross section of the ground. A light brown ant is pictured in the ground along with a microbe. Text to the left of the image reads, "Can a necromenic nematode serve as a biological Trojan horse for an invasive ant?". The names of six professors are listed below the text and image at the bottom left. In the bottom right corner, text reads, "The University of Maine" with "The University of Arizona" below it.

IshaqS.L., A. Hotopp2, S. Silverbrand2, J.E. Dumont, A. Michaud, J. MacRae, S. P. Stock, E. Groden. 2021. Bacterial transfer from Pristionchus entomophagus nematodes to the invasive ant Myrmica rubra and the potential for colony mortality in coastal MaineiScience. In press. Impact 5.08.


The necromenic nematode Pristionchus entomophagus has been frequently found in nests of the invasive European ant Myrmica rubra in coastal Maine, United States, and may contribute to ant mortality and collapse of colonies by transferring environmental bacteria. Paenibacillus and several other bacterial species were found in the digestive tracts of nematodes harvested from collapsed ant colonies. Serratia marcescens, Serratia nematodiphila, and Pseudomonas fluorescens were collected from the hemolymph of nematode-infected wax moth (Galleria mellonella) larvae.

Virulence against waxworms varied by site of origin of the nematodes. In adult nematodes, bacteria were highly concentrated in the digestive tract with none observed on the cuticle. In contrast juveniles had more on the cuticle than in the digestive tract. .  Host species was the primary factor affecting bacterial community profiles, but Spiroplasma sp. and Serratia marcescens sequences were shared across ants, nematodes, and nematode-exposed G. mellonella larvae. 

Research article for young scientists published!

I tried something new last new, I helped rewrite an already published study into a version specifically for young scientists, aged 10-18. Ashkaan Fahimipour, the lead author on the original research article examining the effect of light on bacterial communities in household dust, brought up the idea while we were working together at BioBE.

The journal is called Frontier for Young Minds, and pairs a young scientist with an established scientist to review your articles, a ~1,500 word summary version. The journal provides cartoon illustrations that help bring your science to life.

Ours was written by an undergrad I was mentoring at UO, Sam Rosenberg, and architecture grad student Julia May helped us with our Figures. I wasn’t involved with the original article, but along with Ashkaan, I helped Sam draft the summary as non-technical summaries of highly-technical science can be a real challenge. Check it out!

Rosenberg, S., Ishaq, S., May, J., Fahimipour, A.K. 2020. How light exposure changes bacterial communities in household dust. Frontiers for Young Minds. Article.

DNA double helix with dollar signs as a nucleotide.

The cost of scientific publishing

I’ve published a lot this year. More than normal, since I had 5 months with extra time and the knowledge that I would not be able to devote time to old projects if I began a tenure-track position. It’s been wonderful to publish so many projects, especially ones that had been languishing. But publishing fees can be steep, and often the grant is spent out by the time you publish, leaving researchers struggling to pay to get their results out. The more prestigious the journal, typically; the higher the cost. This encourages many authors to turn to lower impact or less reputable journals, which in turn causes colleagues to be suspicious of the article and may hurt their ability to get more grant money or promotion. On top of the base article processing charge (APC), there may be additional fees to print color photos, supplemental information, or to make the article open-access (readable without a journal subscription).

I’ve published 10 articles in 2019, only a fraction of what I contributed to paying for (thank you, collaborators!!). All costs are presented as 2019 fees in USD. Some journals charge less if you are a member of their society, or have financial assistance, but I’ve included the prices we paid.

Animal: $2835 APC flat rate (includes open-access)

Basic and Applied Ecology: $2000 APC for non-members (includes open-access)

Buildings: $1006 APC (always open-access)

Geoderma: $3350 APC for open-access and $2052.30 for printing 6 figures in color.

Indoor Air: $4300 APC for open-access

Journal of Animal Science: $1300 APC ($100/page member price x 10 pages + $500 color figure charge)

Journal of Exposure Science and Environmental Epidemiology: $3760 APC (includes open-access)

PeerJ: $1095 APC (always open-access). PeerJ also gives discounts for acting as a reviewer, though not applied here.

PLoS Biology: $0 APC for essays because they are published in the magazine (always open access)

PLoS ONE: $1595 APC (always open-access)

Total cost: $21,241

Keep in mind, I’m an editor for two journals and a reviewer for over a dozen, none of which I get paid for. Initial reviews take 2-4 hours, and follow up reviews on revised manuscripts can take 1-2 hours per revision (usually no more than 2 rounds). Editorial takes 1-2 hours per manuscript total, depending on the ease of finding reviewers and the completeness of those reviews. I estimate I’ve provided $3,240 (net) in editorial and review services this year alone.

Microbes and Social Equity essay published!

I’m pleased to announced that the ‘microbes and social equity’ paper has been published as an essay in PLoS Biology, and will be included in their Microbiomes Across Biological Systems special issue.

In summer 2019, I developed and taught a course on ‘Microbes and Social Equity‘ to the Clark Honors College at the University of Oregon. The course assignments were literature review essays on various topics, which were compiled into a single manuscript as the group-based final project for the course. This large version is available as a preprint; however, the published version is more focused.

Framing the discussion of microorganisms as a facet of social equity in human health.

Suzanne L. Ishaq1,2*, Maurisa Rapp2,3, Risa Byerly2,3, Loretta S. McClellan2, Maya R. O’Boyle2, Anika Nykanen2, Patrick J. Fuller2,4, Calvin Aas2, Jude M. Stone2, Sean Killpatrick2,4, Manami M. Uptegrove2, Alex Vischer2, Hannah Wolf2, Fiona Smallman2, Houston Eymann2,5, Simon Narode2, Ellee Stapleton6, Camille C. Cioffi7, Hannah Tavalire8

  1. Biology and the Built Environment Center,  University of Oregon
  2. Robert D. Clark Honors College, University of Oregon
  3. Department of Human Physiology, University of Oregon
  4. Charles H. Lundquist College of Business, University of Oregon
  5. School of Journalism and Communication, University of Oregon
  6. Department of Landscape Architecture, University of Oregon
  7. Counseling Psychology and Human Services, College of Education, University of Oregon
  8. Institute of Ecology and Evolution, University of Oregon


What do ‘microbes’ have to do with social equity? On the surface, very little. But these little organisms are integral to our health, the health of our natural environment, and even impact the ‘health’ of the environments we have built. Early life and the maturation of the immune system, our diet and lifestyle, and the quality of our surrounding environment can all impact our health. Similarly, the loss, gain, and retention of microorganisms ⁠— namely their flow from humans to the environment and back⁠ — can greatly impact our health and well-being. It is well-known that inequalities in access to perinatal care, healthy foods and fiber, a safe and clean home, and to the natural environment can create and arise from social inequality. Here, we focus on the argument that access to microorganisms as a facet of public health, and argue that health inequality may be compounded by inequitable microbial exposure.

Pilot study published on chemicals and bacteria in house dust.

In October 2017, Dr. Rich Corsi came to visit Oregon for two weeks during a sabbatical from the University of Texas, Austin. During his stay, Rich and I, and other BioBE/ESBL researchers chatted about doing a pilot study that would bring UT’s indoor chemistry work together with BioBE’s indoor microbial work.

Since we began our collaboration in the fall of 2017, only one of the research team is still in their original position (Jeff Kline at ESBL)! Rich Corsi, Ying Xu, and myself have all gone on to faculty positions elsewhere, graduate student Chenyang Bi defended and started a post-doc position, and the two undergrads working with me, Susie Nunez and Samantha Velazquez, graduated and went on to other things! Science collaborations work best when they can stand the test of time and geography. The benefit to everyone moving around is that you are able to hold collaboration meetings in new and exciting places each time.

In addition to the literature review we collaborated on, we eventually did get a research pilot running, and it has now been published in PeerJ!

Accumulation of di-2-ethylhexyl phthalate from polyvinyl chloride flooring into settled house dust and the effect on the bacterial community.

Samantha Velazquez1, Chenyang Bi 2,3, Jeff Kline 1,4, Susie Nunez1, Richard Corsi 3,5, Ying Xu 3,6, Suzanne L. Ishaq1,7*


1 Biology and the Built Environment Center,  University of Oregon, Eugene, OR, 97403

2 Department of Civil Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 (current)

3 Department of Civil, Architectural and Environmental Engineering, University of Texas, Austin, TX 78712

4 Energy Studies and Buildings Laboratory, University of Oregon, Eugene, OR, 97403

5 Fariborz Maseeh College of Engineering and Computer Science, Portland State University, Portland, OR 97207 (current)

6 Department of Building Science, Tsinghua University, 100084, Beijing, P. R. China (current)

7 School of Food and Agriculture, University of Maine, Orono, ME 04469 (current)


Di-2-ethylhexyl phthalate (DEHP) is a plasticizer used in consumer products and building materials, including polyvinyl chloride flooring material. DEHP adsorbs from material and leaches into soil, water, or dust, and presents an exposure risk to building occupants by inhalation, ingestion, or absorption.  A number of bacterial isolates are demonstrated to degrade DEHP in culture, but bacteria may be susceptible to it as well, thus this study examined the relation of DEHP to bacterial communities in dust.  Polyvinyl chloride flooring was seeded with homogenized house dust and incubated for up to 14 days, and bacterial communities in dust were identified at days 1, 7, and 14 using the V3-V4 regions of the bacterial 16S rRNA gene.  DEHP concentration in dust increased over time, as expected, and bacterial richness and Shannon diversity were negatively correlated with DEHP concentration.  Some sequence variants of Bacillus, Corynebacterium jeddahense, Streptococcus, and Peptoniphilus were relatively more abundant at low concentrations of DEHP, while some Sphingomonas, Chryseobacterium, and a member of the Enterobacteriaceae family were relatively more abundant at higher concentrations.  The built environment is known to host lower microbial diversity and biomass than natural environments, and DEHP or other chemicals indoors may contribute to this paucity.

Paper published on effect of farming systems on soil bacteria!

After several years of bouncing through internal and external review, I’m pleased to announce that the first microbes paper out of the Montana State University Fort Ellis project has been published in Geoderma! The Fort Ellis research has encompassed multiple labs, projects, and many personnel, as it was a large collaboration looking at the effect of different farming systems on biodiversity at the macro (plant), mini (insect), and micro (-be) levels. Spanning multiple years, this project has been a massive undertaking that I briefly participated in but anticipate getting four publications out of (two more are in preparation).

Winter wheat

I previously presented this work at the 2017 Ecological Society of America (ESA) conference (poster: Ishaq et al ESA 2017 poster). And this field soil was the “soil probiotic” that was used in the follow-up greenhouse trial that I ran which was also published this year.

Soil bacterial communities of wheat vary across the growing season and among dryland farming systems.

Ishaq, S.L., Seipel, T., Yeoman, C.J., Menalled, F.D. 2020. Geoderma 358:113989.


Despite knowledge that management practices, seasonality, and plant phenology impact soil microbiota; farming system effects on soil microbiota are not often evaluated across the growing season.  We assessed the bacterial diversity in soil around wheat roots through the spring and summer of 2016 in winter wheat (Triticum aestivium L.) in Montana, USA, from three contrasting farming systems: a chemically-managed no-tillage system, and two USDA-certified organic systems in their fourth year, one including tillage and one where sheep grazing partially offsets tillage frequency. Bacterial richness (range 605 – 1174 OTUs) and evenness (range 0.80 – 0.92) peaked in early June and dropped by late July (range 92 – 1190, 0.62-0.92, respectively), but was not different by farming systems.  Organic tilled plots contained more putative nitrogen-fixing bacterial genera than the other two systems.  Bacterial community similarities were significantly altered by sampling date, minimum and maximum temperature at sampling, bacterial abundance at date of sampling, total weed richness, and coverage of Taraxacum officinale, Lamium ampleuxicaule, and Thlaspi arvense.  This study highlights that weed diversity, season, and farming management system all influence soil microbial communities. Local environmental conditions will strongly condition any practical applications aimed at improving soil diversity, especially in semi-arid regions where abiotic stress and seasonal variability in temperature and water availability drive primary production. Thus, it is critical to incorporate or address seasonality in soil sampling for microbial diversity.