Expanding uses for bioengineered bacterial spores

Fused to the outer layer of bacterial spores, things like enzymes, biosensors, and drugs are easily stored under even extreme conditions

Tufts University

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“Spore engineering is still an emerging technology,” said Nik Nair. “Most products are in the development stage and are not ready for widespread commercial application. We are hopeful that expanding the target list for fusion can speed up this process.”

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Credit: Geoman3

A remarkable quality of bioengineering is the fact that scientists can take biological processes honed by millions of years of evolution and use them to efficiently create drugs, chemicals, and other products to improve our lives. Now Tufts researchers have found new ways to expand the potential for using bacterial spores as catalysts for chemical reactions, biofuel production, or breaking down pollutants.

When some species of bacteria find themselves in an environmentally stressful situation like extreme heat, cold, aridity, loss of nutrients, or even exposure to disinfectants, they can hunker down and form spores—hardened protein-coated spheres protecting a DNA-filled core. The spores remain stable and dormant for years—even centuries—waiting patiently until the right conditions allow them to resurrect into active bacteria once again.

This extraordinary stability has made bacterial spores great candidates for bioengineering. Researchers are designing spores to express drugs, industrial enzymes, and catalysts, and be used as biological sensors, as useful molecules are fused to the spore’s outer coat of proteins. The products fused to the proteins can be stored and distributed without the need for refrigeration, or can be used in applications under extreme conditions, such as high heat or exposure to harsh chemicals.

While promising, the technology has encountered hurdles, including the fact that only 12 of the nearly 50 proteins that coat spores have been explored as potential objects to fuse with new substances. 

Now Nik Nair, associate professor of chemical and biological engineering, and his team have expanded the list of fusion candidates to as many as 33 of the proteins that coat bacterial spores, suggesting an approach that might lead to a much wider range of bioengineered products. They describe the work in a paper in the journal JACS Au.

“Spore engineering is still an emerging technology,” said Nair. “Most products are in the development stage and are not ready for widespread commercial application. We are hopeful that expanding the target list for fusion can speed up this process.”

The types of bacterial spore products could include oral vaccine delivery, for example, where spores with antigens on their surface pass through the gastrointestinal tract to stimulate a mucosal immune response. This makes them highly attractive for distribution to remote locations without needing refrigeration and for needle-free vaccination.

The spores can also be engineered to glow due to fluorescence in the presence of specific chemical compounds, making them great candidates for detecting toxins in harsh environments. 

Pollution Cleanup Potential

By displaying enzymes on their surface, engineered spores can also function as catalysts for chemical reactions, biofuel production, or breaking down pollutants. 

As a proof of concept, Nair and his research team fused the outer spore proteins with enzymes that can degrade polyethylene terephthalate (PET), a hard plastic used in many products like water bottles and automotive parts.

To do this, they surveyed their expanded list of spore proteins to find the most stable and effective fusion product. For the PET-dissolving enzyme, the small spore coat assembly protein A (SscA) was the best of 33 proteins they tested for fusion. It yielded fourfold higher activity than any other fusion, breaking down the monomers of PET. On actual PET solid plastic, the enzyme fused to the outer coat protein Y (CotY) yielded higher activity, consistent with the fact that it is more accessible on the surface of the spore’s outer coat.

The researchers also suggest that combining fusion products in spores might be a way to create a multi-step process of breaking down solid plastics and then metabolizing the released chemicals further into environmentally safe forms.

As bioengineered spores make their way toward commercial applications, a key question is whether the spores can be prevented from reactivating as bacteria when released in the environment.

“We have a good understanding of what activates spores to become replicating bacteria again,” said Nair. “If we delete five specific genes, they’ll never germinate and always remain spores. Product safety will be a critical part of introducing spores to widespread applications.” 

Nair suggested that SscA, CotY, and other spore proteins could be candidates for more bioengineered products. Continuing development of this technology is being carried out by a new startup company emerging from this research, called Caravel Bio, led by Trevor Nicks, EG23, a former graduate student in Nair’s lab and co-author of the study. Todd Chappell, former postdoctoral researcher in the Nair lab was the first author of this study.

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Journal

Journal of the American Chemical Society

DOI

10.1021/jacsau.6c00594 

Method of Research

Experimental study

Subject of Research

Cells

Article Title

Advancing Protein Display on Bacterial Spores through an Extensive Survey of Coat Components

 

Canadian wildfire smoke linked to fewer bird sightings in New York State

Wildfire smoke alters observations of 65% of breeding bird species in New York State

UB study compared air quality data with birdwatching reports, including during historic 2023 wildfire season

University at Buffalo

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BUFFALO, N.Y. — Despite burning hundreds of miles away, Canadian wildfires have become a familiar source of disruption in New York State. 

Air quality advisories. A spike in emergency room visits for asthma.

Now, a University at Buffalo study has identified another consequence: fewer sightings of dozens of bird species across the Empire State. 

In a study published earlier this month in Biodiversity and Conservation, a Springer Nature journal, researchers found that 40 different bird species were less likely to be observed in New York as levels of fine particulate matter (PM2.5) in the air increased during recent breeding seasons. The analysis included the 2023 season that overlapped with Canada’s worst wildfire season on record. 

“Our results show a link between wildfire smoke and the probability of observing particular bird species,” says corresponding author Festus Adegbola, a PhD candidate in the Department of Geography, within the UB College of Arts and Sciences. “Wildfire smoke is often underexplored when monitoring biodiversity. Failing to account for air quality may bias models of species distributions and abundance.”

The researchers first analyzed PM2.5 levels, a key marker of wildfire smoke, during New York's 2021–2023 breeding seasons. The highest concentrations occurred in 2023, when smoke from Canada’s historic wildfires degraded air quality across New York throughout June and July. PM2.5 levels exceeded World Health Organization guidelines on multiple occasions, at times reaching eight times the recommended limit.

The researchers then matched the PM2.5 data with nearly 99,000 birdwatching checklists submitted to Cornell University's eBird database. The citizen science project, run by the Cornell Lab of Ornithology, allows birdwatchers to record the birds they observe, creating one of the world's largest collections of bird observations. 

Because the observations come from birdwatchers with varying levels of experience, the UB researchers used rigorous data filtering and statistical methods to ensure reliable results.

In all, they analyzed 84 different bird species across nearly 99,000 eBird checklists collected across all of New York during the three recent breeding seasons. 

Nearly half of the species studied were less likely to be observed when PM2.5 rose. These included many migratory forest songbirds, such as warblers, thrushes and vireos.

“It’s possible that smoky conditions changed the birds’ behavior — singing and moving less, spending more time in dense forest canopy — and therefore made them harder to detect,” Adegbola says.

However, 15 species were actually more likely to be observed as PM2.5 levels rose, while another 29 showed no significant change in how likely they were to be observed. These included many aerial insectivores and some wetland-associated birds.

That doesn’t necessarily mean wildfire smoke benefited those birds.

“These species often occupy more open environments than forest songbirds, so it’s possible their increased sightings had more to do with where birdwatchers chose to observe during smoky conditions than how the birds themselves responded,” says co-author Adam Wilson, PhD, associate professor of geography and Adegbola’s adviser. 

The findings suggest that fewer bird sightings during smoky periods don't necessarily mean there are fewer birds — they may simply be harder to detect. Understanding that distinction is crucial for biodiversity monitoring so that temporary declines in detectability aren't mistaken for true population declines. 

“Still, as climate change continues to intensify wildfires, it’s crucial we understand how birds will be affected by increased smoke pollution,” Wilson says. “This study is hopefully a first step to better understanding how species respond to wildfire smoke exposure.”

Other co-authors include Stuart Evans, PhD, assistant professor of geography, and Olivia Sanderfoot, PhD, a research scientist with the Cornell Lab of Ornithology. 

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Journal

Biodiversity and Conservation

DOI

10.1007/s10531-026-03406-9 

Method of Research

Data/statistical analysis

Subject of Research

Animals

Article Title

Wildfire smoke alters observations of 65% of breeding bird species in New York State

 

Forest rivers remove nitrogen through seasonally shifting natural processes

New study shows that microorganisms, water chemistry, altitude, and land use work together to regulate nitrogen removal across summer and winter

Shenyang Agricultural University Collaborative Journals

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Geographical and micro-environmental factors regulate nitrogen removal in a forest-dominated river

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Credit: Wenshi Zhang, Xiaodong Li, Hao Jiang, & Quanfa Zhang

Rivers do more than transport water across landscapes. They also act as natural filters, transforming excess nitrogen before it reaches downstream lakes, reservoirs, and coastal waters. A new study of a forest-dominated river in central China reveals that this filtering capacity is controlled by a changing combination of microbial activity, water and sediment conditions, altitude, and surrounding land use.

“Our findings show that riverine nitrogen removal cannot be explained by a single environmental factor,” said corresponding author Hao Jiang of the Wuhan Botanical Garden, Chinese Academy of Sciences. “The dominant controls change with the seasons, so effective watershed management must consider both large-scale landscape conditions and the microscopic processes occurring within river sediments.”

Excess reactive nitrogen from fertilizer use, sewage, and industrial activity can contribute to eutrophication, harmful algal blooms, oxygen depletion, and biodiversity loss. Rivers help reduce this pollution through microbial processes that convert biologically available nitrogen into harmless nitrogen gas, which is released into the atmosphere.

The researchers focused on two major nitrogen-removal pathways: denitrification and anaerobic ammonium oxidation, commonly known as anammox. They collected water and surface sediment samples from 18 sites along the Jinshui River during summer and winter. The catchment covers approximately 730 square kilometers, spans a large elevation range, and has more than 95% forest cover in much of its upper reaches.

To understand nitrogen cycling across multiple scales, the team combined remote sensing, nitrogen-15 isotope labeling, measurements of water and sediment chemistry, and quantitative polymerase chain reaction analysis of microbial functional genes.

Denitrification was the dominant nitrogen-removal pathway in both seasons. It accounted for about 90% of total measured nitrogen removal in summer and 95% in winter. Average denitrification rates were substantially higher during summer, while anammox contributed a smaller but measurable share of nitrogen removal throughout the year.

The analysis also revealed a strong seasonal shift in the factors controlling these processes. During summer, denitrification was closely associated with microbial functional genes and local sediment conditions, including total nitrogen, organic carbon, carbon-to-nitrogen ratio, and moisture. Water properties indirectly influenced denitrification by shaping sediment conditions and the abundance of nitrogen-cycling microorganisms.

Anammox responded differently. In summer, its activity was influenced more strongly by geographical factors, particularly altitude and land use. Greater forest cover was associated with higher anammox rates, possibly because the relatively low availability of organic carbon in forested areas reduced competition from denitrifying microorganisms.

In winter, water chemistry became the primary control on both denitrification and anammox. Temperature and concentrations of ammonium and nitrate in the overlying water played especially important roles. Lower temperatures reduced microbial activity and weakened the internal recycling of nitrogen within sediments. As a result, nitrogen supplied by the river water became more important as a substrate for microbial removal.

The researchers also found that nitrification and denitrification were closely linked during summer, suggesting that nitrogen compounds produced by one microbial process helped fuel another. This connection weakened during winter, when cold conditions reduced microbial activity and limited the movement of chemical substrates between sediment zones.

The study demonstrates that catchment geography and microscopic sediment processes must be considered together to understand how rivers regulate nitrogen pollution. The findings could help improve models of the global nitrogen cycle and support more seasonally responsive strategies for managing forested watersheds, land-use change, and downstream water quality.

 

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Journal Reference: Zhang W, Li X, Jiang H, Zhang Q. 2026. Geographical and micro-environmental factors regulate nitrogen removal in a forest-dominated river. Nitrogen Cycling 2: e020 doi: 10.48130/nc-0026-0007  

https://www.maxapress.com/article/doi/10.48130/nc-0026-0007  

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About Nitrogen Cycling:
Nitrogen Cycling (e-ISSN 3069-8111) is a multidisciplinary platform for communicating advances in fundamental and applied research on the nitrogen cycle. It is dedicated to serving as an innovative, efficient, and professional platform for researchers in the field of nitrogen cycling worldwide to deliver findings from this rapidly expanding field of science.

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Journal

Nitrogen Cycling

DOI

10.48130/nc-0026-0007 

Method of Research

Experimental study

Article Title

Geographical and micro-environmental factors regulate nitrogen removal in a forest-dominated river

Human activities compromise coral health and resilience

University of Hawaii at Manoa

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First author Zachary A. Quinlan taking water samples for metabolomics.

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Credit: UH Mānoa/ SOEST/ HIMB

Human activities are fundamentally altering the chemical makeup of local coral reefs, according to a study led by the University of Hawai‘i at Mānoa and published recently in Nature Communications. The research team discovered that 25 contaminants from agricultural, industrial, and pharmaceutical sources accumulated in the soft tissues of coral around Maui, Hawai‘i. Additionally, in areas impacted by human activities, the energy and nutrient availability within the coral’s tissue decreases, making them significantly less resilient to environmental stressors such as warmer or acidic waters.

“Our findings suggest that monitoring the pool of chemicals within the coral tissues, called metabolomes, can serve as a powerful tool for tracking the hidden impacts of anthropogenic disturbance on marine life,” said Zach Quinlan, lead author and research biologist at the Hawai‘i Institute of Marine Biology in the UH Mānoa School of Ocean and Earth Science and Technology.

Quinlan and an international team of researchers tested the metabolomes of 380 lobe corals (Porites lobata) and rice corals (Montipora capitata) from 16 sites off west and south Maui. They found that human activities both within the adjacent watershed and in the marine ecosystem altered the composition of the corals’ metabolomes. In areas with more ecosystem disturbance, there was increased accumulation of contaminants and a decrease of nutrient and energy reserves in the coral tissues.

“It was extremely surprising that the metabolomes of both coral species had almost identical trends,” said Quinlan. “These corals have very different life strategies, and we wouldnʻt normally expect them to accumulate contaminants the same or even necessarily respond the same to disturbances. This demonstrates how strong of a forcing these anthropogenic activities really are.”

Clues from the 2016 bleaching event

Using historical trends in coral cover from five of the sites they sampled, the team found that sites that had the most severe declines in coral cover after the 2016 bleaching event are the sites with the most impacted metabolomes. At more impacted sites, nitrogen and energy reserves were reduced, while stress chemicals were enriched.

The research team proposed two potential mechanisms by which human activities and contamination of marine environments lead to decreased coral resilience: 1) accumulation of anthropogenic molecules such as pharmaceuticals and industrial byproducts, and 2) increased pressure from anthropogenic activities requires coral to utilize portions of their nitrogen and energetic reserves.

“This response to anthropogenic pressure makes the coral less resilient to stressors,” said Quinlan. “Together, our findings suggest a direct relationship between anthropogenic disturbance, accumulation of dangerous contaminants within corals, and coral health that is consistent across species.”

Tracing contaminants through the ecosystem

The researchers propose that monitoring the metabolomes of coral or other coastal seafloor species can be used as a powerful tool to track human impacts on natural ecosystems. 

“Beyond the implications for coral health and resilience, this study demonstrates how many anthropogenic contaminants are escaping into marine ecosystems,” Megan Donahue, senior author on the paper and HIMB director. “We see increasing evidence that anthropogenic contaminants have broad cumulative impacts, undermining the resilience of coastal ecosystems.”

This study underscores the urgent need to reduce human impacts to the marine environment, to protect marine and human health. Looking ahead, Quinlan and team are searching for ways to enrich coral tissue nitrogen and energy reserves in controlled experiments to determine whether those increases lead to more resilient corals.

Additional co-authors include researchers from Woods Hole Oceanographic Institution, University of Newcastle (Australia), University of New South Wales (Australia), Bio21 Molecular Science and Biotechnology Institute (Australia), The Nature Conservancy, University of California Merced, Princeton University, James Cook University (Australia). 

 

Coral reef.

Credit

Tiara Stark/TNC

 

Olowalu coral reef, coastal shot

Credit

Drew Sulock

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Journal

Nature Communications

DOI

10.1038/s41467-026-74960-7 

Method of Research

Observational study

Article Title

Coral metabolome quality and contaminant loads track human land use

Article Publication Date

15-Jul-2026

COI Statement

Author B.N. is an employee of Metabolomics Australia, the facility contracted to provide tandem mass spectrometry services for this work. Authors declare that they have no further competing interests.

Global study reveals how shipping and human activity shape bacteria in port waters

Analysis of more than 16 million DNA sequences shows that port size, wastewater discharge, geography, and maritime activity are closely associated with the structure of bacterial communities worldwide

Shenyang Agricultural University Collaborative Journals

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A global synthesis of port water microbiome biogeography and anthropogenic associations

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Credit: Baoyi Lv, Qitong Zhang, Tingxuan An, Shenglong Mei, Guolin Kan, Dong Wu & Jianhong Shi

Ports connect cities, economies, and supply chains, but they also create environments where marine ecosystems interact intensely with shipping, wastewater, and coastal development. A new global study has revealed that these pressures leave measurable signatures in the microscopic communities living in port waters.

“Port microorganisms are not only essential contributors to marine nutrient cycling, but also sensitive indicators of environmental change and human influence,” said corresponding author Jianhong Shi of Shanghai Maritime University. “By examining ports across multiple continents, we were able to identify shared ecological patterns while also showing how shipping and wastewater may influence microbial diversity and potential pathogen abundance.”

The researchers conducted a large-scale synthesis of bacterial communities in port waters from 23 cities in eight countries across five continents. They analyzed 1,045 water samples containing more than 16.5 million high-quality 16S rRNA gene sequences, allowing them to compare microbial diversity, geographic distribution, ecological assembly processes, and possible sources of bacteria.

The results showed a clear distance-decay pattern. In other words, bacterial communities from ports located closer together tended to be more similar, while similarity decreased as geographic distance increased. However, this relationship was weaker in high-capacity ports, suggesting that frequent shipping activity may help transport microorganisms between distant locations, potentially through ballast water or organisms attached to ship surfaces.

Bacterial richness did not follow the familiar pattern often observed in plants and animals, where biodiversity is generally highest in tropical regions. Instead, port-water bacterial richness peaked at mid-latitudes, although latitude explained only a small portion of the overall variation.

Across the global dataset, the researchers identified 12 core bacterial genera, together accounting for nearly one-quarter of the bacterial community. The most abundant was SAR11 subclade IIIa, a widespread marine lineage involved in carbon cycling. Other core groups may contribute to the degradation of organic matter and the cycling of nitrogen and sulfur.

The study also detected 295 distinct potential pathogenic bacterial variants, representing approximately 6% of the analyzed sequences. Their abundance and composition differed substantially among regions, with African port samples showing the highest relative abundance of potential pathogens. Some pathogen-related sequences were geographically restricted. For example, sequences associated with Vibrio parahaemolyticus, a bacterium linked to seafood-borne illness, were detected only in Asian samples.

The authors emphasized that DNA-based identification indicates the presence of sequences associated with potential pathogens, rather than confirming that viable disease-causing organisms were active in every sample.

Source-tracking analysis suggested that air and human-associated sources were major contributors to port-water bacterial communities. Human excretion accounted for an estimated 26.6% of the potential bacterial sources, while air contributed 26.9%.

Wastewater discharge was associated with lower bacterial diversity and greater potential pathogen abundance. Port capacity showed the strongest individual correlation with bacterial community structure and was also positively associated with pathogen abundance. These findings indicate that both land-based pollution and maritime operations can influence port microbiomes.

The researchers found that deterministic ecological processes, including environmental selection by factors such as salinity, temperature, pH, and dissolved oxygen, played a larger role than random processes in shaping global port bacterial communities.

The findings support the use of microbial communities as sensitive indicators of port ecosystem health and highlight the need for stronger wastewater management, pathogen surveillance, and ballast-water controls. The authors also recommend standardized global sampling and more advanced methods, including metagenomics and full-length gene sequencing, to improve future identification of microorganisms and their ecological functions.

 

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Journal reference: Lv B, Zhang Q, An T, Mei S, Kan G, et al. 2026. A global synthesis of port water microbiome biogeography and anthropogenic associations. Biocontaminant 2: e008 doi: 10.48130/biocontam-0026-0005  

https://www.maxapress.com/article/doi/10.48130/biocontam-0026-0005  

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About Biocontaminant:
Biocontaminant (e-ISSN: 3070-359X) is a multidisciplinary platform dedicated to advancing fundamental and applied research on biological contaminants across diverse environments and systems. The journal serves as an innovative, efficient, and professional forum for global researchers to disseminate findings in this rapidly evolving field.

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Journal

Biocontaminant

DOI

10.48130/biocontam-0026-0005 

Method of Research

Experimental study

Article Title

A global synthesis of port water microbiome biogeography and anthropogenic associations