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1. Modern buildings act as a dynamic source and sink for urban air pollutants

   https://doi.org/10.1016/j.crsus.2024.100103  

   Wu, Tianren; Tasoglou, Antonios; Wagner, Danielle N; Jiang, Jinglin; Huber, Heinz J; Stevens, Philip S; Jung, Nusrat; Boor, Brandon E (May 2024, Cell Reports Sustainability)

   Science for Society Buildings account for a significant fraction of the land area in cities and actively exchange air with their proximate outdoor environments via mechanical ventilation systems. However, the direct impact of buildings on urban air pollution remains poorly characterized. Due to reductions in traffic-associated emissions of volatile organic compounds (VOCs), volatile chemical products, which are widely used inside buildings, have become a major VOC source in urban areas. Indoor-generated VOCs are likely to be an important contributor to the VOC burden of the urban atmosphere, and ventilation systems provide a pathway for VOCs to be released outdoors. Here, we show how modern buildings act as significant emission sources of VOCs for the outdoor environment. Our results demonstrate that future air quality monitoring efforts in cities need to account for direct VOC discharge from buildings in order to capture emerging sources of environmental pollution that can impact the climate and human health. Summary Urban air undergoes transformations as it is actively circulated throughout buildings via ventilation systems. However, the influence of air exchange between outdoor and indoor atmospheres on urban air pollution is not well understood. Here, we quantify how buildings behave as a dynamic source and sink for urban air pollutants via high-resolution online mass spectrometry measurements. During our field campaign in a high-performance office building, we observed that the building continually released volatile organic compounds (VOCs) into the urban air and removed outdoor ozone and fine particulate matter. VOC emissions from people, their activities, and surface reservoirs result in significant VOC discharge from the building to the outdoors. Per unit area, building emissions of VOCs are comparable to traffic, industrial, and biogenic emissions. The building source-sink behavior changed dynamically with occupancy and ventilation conditions. Our results demonstrate that buildings can directly influence urban air quality due to substantial outdoor-indoor air exchange. 

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2. Perspective: Simple State Communities to Study Microbial Interactions: Examples and Future Directions

   https://doi.org/10.3389/fmicb.2022.801864  

   Sarkar, Soumyadev; Ward, Kaitlyn; Kamke, Abigail; Ran, Qinghong; Feehan, Brandi; Richie, Tanner; Reese, Nicholas; Lee, Sonny T. (January 2022, Frontiers in Microbiology)

   Microbial interactions in natural environments are intricately complex. High numbers and rich diversity of microorganisms, along with compositional heterogeneities complicate the cause. It is essential to simplify these complex communities to understand the microbial interactions. We proposed a concept of “ simple state community ,” which represents a subset of microbes and/or microbial functions of the original population that is necessary to build a stable community. By combining microbial culturing and high-throughput sequencing, we can better understand microbe-microbe and microbe-host interactions. To support our proposed model, we used carbon-based and nitrogen-based media to capture the simple state communities. We used 16S rRNA amplicon sequencing and assigned taxonomic identity to the bacterial populations before and after simple state communities. We showed that simple state communities were a subset of the original microbial communities at both phyla and genera level. We further used shotgun metagenomics to gain insights into the functional potential of the assembled simple state communities. Our proposed model supported the goal of simplifying the complex communities across diverse systems to provide opportunity to facilitate comprehension of both the structure and function of the subset communities. Further applications of the concept include the high-throughput screening of simple state communities using the BIOLOG ® system and continuous culturing (Chemostat). This concept has the potential to test diverse experimental hypotheses in simplified microbial communities, and further extend that knowledge to answer the overarching questions at a more holistic level. 

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3. Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity

   https://doi.org/10.1038/s41564-022-01266-x  

   Shaffer, Justin P.; Nothias, Louis-Félix; Thompson, Luke R.; Sanders, Jon G.; Salido, Rodolfo A.; Couvillion, Sneha P.; Brejnrod, Asker D.; Lejzerowicz, Franck; Haiminen, Niina; Huang, Shi; et al (December 2022, Nature Microbiology)

   Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a diverse set of 880 microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments, thus allowing us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of an evolving community resource. We demonstrate the utility of this database by testing the hypothesis that every microbe and metabolite is everywhere but the environment selects. Our results show that metabolite diversity exhibits turnover and nestedness related to both microbial communities and the environment, whereas the relative abundances of microbially related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain chemistry, in particular terpenoids, in distinguishing Earth’s environments (for example, terrestrial plant surfaces and soils, freshwater and marine animal stool), as well as that of certain microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and Pantoea dispersa (terrestrial plant detritus). This Resource provides insight into the taxa and metabolites within microbial communities from diverse habitats across Earth, informing both microbial and chemical ecology, and provides a foundation and methods for multi-omics microbiome studies of hosts and the environment. 

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4. Survey of pond habitats and aquatic diversity of Madison, Wisconsin from May to Aug 2019 and 2020 Data Set

   https://doi.org/10.6073/pasta/216bc17b3e9a24994119d4ff3039e6a1  

   Trovillion, Daniel; Saur, Erin (January 2023, Environmental Data Initiative)

   1) Urbanization may lead to changes in local richness (alpha diversity) or in community composition (beta diversity), although the direction of change can be challenging to predict. For instance, introduced species may offset the loss of native specialist taxa, leading to no change in alpha diversity in urban areas, but decreased beta diversity (i.e., more homogenous community structure). Alternatively, because urban areas can have low connectivity and high environmental heterogeneity between sites, they may support distinct communities from one another over small geographic distances. 2) Wetlands and ponds provide critical ecosystem services and support diverse communities, making them important systems in which to understand consequences of urbanization. To determine how urban development shapes pond community structure, we surveyed 68 ponds around Madison, Wisconsin, USA, which were classified as urban, greenspace, or rural based on surrounding land use. We evaluated the influence of local abiotic factors, presence of nonnative fishes, and landscape characteristics on alpha diversity of aquatic plants, macroinvertebrates, and vertebrates. We also analyzed whether surrounding land cover was associated with changes in community composition and/or the presence of specific taxa. 3) We found a 23% decrease in mean richness (alpha diversity) from rural to urban pond sites, and a 15% decrease in richness from rural to urban greenspace pond sites. Among landscape factors, observed pond richness was negatively correlated with adjacent developed land and mowed lawns, as well as greater distances to other waterbodies. Among pond level factors, habitat complexity was associated with increased richness, while the presence of invasive fish was associated with decreased richness. 4) Beta diversity was relatively high for all ponds due to turnover in composition between sites. Urban ponds supported more introduced species, lacked a subset of native species found in rural ponds, and had slightly higher beta diversity than greenspace and rural ponds. 5) Synthesis and Applications: Integrating ponds into connected greenspaces comprised of native vegetation (rather than mowed grass), preventing nonnative fish introductions, and promoting habitat complexity may mitigate negative effects of urbanization on aquatic richness. The high beta diversity of distinct pond communities emphasizes their importance to biodiversity support in urban environments, despite being small in size and rarely incorporated into urban conservation planning. 

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5. Survey of pond habitats and aquatic diversity of Madison, Wisconsin from May to Aug 2019 and 2020 Data Set

   https://doi.org/10.6073/pasta/262866936bb8cffb3ff1d9faa9a04a93  

   Trovillion, Daniel; Sauer, Erin (January 2023, Environmental Data Initiative)

   1) Urbanization may lead to changes in local richness (alpha diversity) or in community composition (beta diversity), although the direction of change can be challenging to predict. For instance, introduced species may offset the loss of native specialist taxa, leading to no change in alpha diversity in urban areas, but decreased beta diversity (i.e., more homogenous community structure). Alternatively, because urban areas can have low connectivity and high environmental heterogeneity between sites, they may support distinct communities from one another over small geographic distances. 2) Wetlands and ponds provide critical ecosystem services and support diverse communities, making them important systems in which to understand consequences of urbanization. To determine how urban development shapes pond community structure, we surveyed 68 ponds around Madison, Wisconsin, USA, which were classified as urban, greenspace, or rural based on surrounding land use. We evaluated the influence of local abiotic factors, presence of nonnative fishes, and landscape characteristics on alpha diversity of aquatic plants, macroinvertebrates, and vertebrates. We also analyzed whether surrounding land cover was associated with changes in community composition and/or the presence of specific taxa. 3) We found a 23% decrease in mean richness (alpha diversity) from rural to urban pond sites, and a 15% decrease in richness from rural to urban greenspace pond sites. Among landscape factors, observed pond richness was negatively correlated with adjacent developed land and mowed lawns, as well as greater distances to other waterbodies. Among pond level factors, habitat complexity was associated with increased richness, while the presence of invasive fish was associated with decreased richness. 4) Beta diversity was relatively high for all ponds due to turnover in composition between sites. Urban ponds supported more introduced species, lacked a subset of native species found in rural ponds, and had slightly higher beta diversity than greenspace and rural ponds. 5) Synthesis and Applications: Integrating ponds into connected greenspaces comprised of native vegetation (rather than mowed grass), preventing nonnative fish introductions, and promoting habitat complexity may mitigate negative effects of urbanization on aquatic richness. The high beta diversity of distinct pond communities emphasizes their importance to biodiversity support in urban environments, despite being small in size and rarely incorporated into urban conservation planning. 

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