The end of microbiology

Reciprocal Inclusion of Microbiomes and Environmental Justice Contributes Solutions to Global Environmental Health Challenges

Generations of colonialism, industrialization, intensive agriculture, and anthropogenic climate change have radically altered global ecosystems and by extension, their environmental microbiomes. The environmental consequences of global change disproportionately burden racialized communities, those with lower socioeconomic status, and other systematically underserved populations. Environmental justice seeks to balance the relationships between environmental burden, beneficial ecosystem functions, and local communities. Given their direct links to human and ecosystem health, microbes are embedded within social and environmental justice. Considering scientific and technological advances is becoming an important step in developing actionable solutions to global equity challenges. Here we identify areas where inclusion of microbial knowledge and research can support planetary health goals. We offer guidelines for strengthening a reciprocal integration of environmental justice into environmental microbiology research. Microbes form intimate relationships with the environment and society, thus microbiologists have numerous and unique opportunities to incorporate equity into their research, teaching, and community engagement.

Words Are Essential, but Underexamined, Research Tools for Microbes and Microbiomes

Language constitutes an essential set of scientific construction tools, not only for communicating knowledge, but for conceptualizing the world. Metaphors in particular, as conventions that guide and reproduce analogical reasoning, merit attention that they largely do not receive. My research addresses this deficit by examining how metaphors for handling microbes shape possibilities for working with yeast and bacteria in synthetic biology, microbiome research, and other fields that reconfigure what microbes can be. Though poised to reexamine assumptions, these fields routinely rest on metaphors and other language tools that quietly embed ways of thinking that may work against wider aims-for example, imagining bacteria as imperfect machines that should therefore be rendered increasingly passive and controllable. Researchers, therefore, need to examine how language tools structure their observations and expectations so that the tools they choose are appropriate for the work they want to do.

La milpa como modelo para el estudio de la microbiodiversidad e interacciones planta-bacteria

La microbiología agrícola busca reemplazar a los agroquímicos por microorganismos o sus productos como agentes de control biológico, debido a que el uso de tecnologías de la revolución verde tiene efectos negativos sobre el ambiente, los productores y sus familias, los consumidores y la salud de los cultivos. Sin embargo, el conocimiento actual acerca de las interacciones benéficas planta-bacteria en ambientes complejos es limitado e insuficiente, para lograr el éxito esperado de los productos biológicos. Las milpas son agroecosistemas tradicionales donde se cultivan diversas variedades de maíz nativo con otras especies asociadas; no se utiliza riego, ni labranza y aunque su aplicación va en aumento, comúnmente no se utilizan agroquímicos; por esto, la milpa representa una fuente de conocimiento sobre prácticas sustentables. Recientemente, se han descrito cambios en las comunidades microbianas de los sistemas agrícolas a causa de la modernización y a la domesticación de las plantas. En la milpa, también se han identificado interacciones benéficas planta-bacteria que parecen haberse perdido en los cultivos modernos. En esta revisión, discutimos las estrategias clásicas y modernas de la microbiología agrícola que pueden ser aplicadas en el estudio de la milpa. El establecimiento de la milpa como modelo de estudio de las interacciones planta-bacteria puede resultar en la generación del conocimiento necesario para disminuir el uso de agroquímicos en los sistemas agrícolas modernos, así como evitar su creciente uso en las milpas.

Global cellulose biomass, horizontal gene transfers and domain fusions drive microbial expansin evolution

Plants must rearrange the network of complex carbohydrates in their cell walls during normal growth and development. To accomplish this, all plants depend on proteins called expansins that nonenzymatically loosen noncovalent bonding between cellulose microfibrils. Surprisingly, expansin genes have more recently been found in some bacteria and microbial eukaryotes, where their biological functions are largely unknown. Here, we reconstruct a comprehensive phylogeny of microbial expansin genes. We find these genes in all eukaryotic microorganisms that have structural cell wall cellulose, suggesting expansins evolved in ancient marine microorganisms long before the evolution of land plants. We also find expansins in an unexpectedly high diversity of bacteria and fungi that do not have cellulosic cell walls. These bacteria and fungi inhabit varied ecological contexts, mirroring the diversity of terrestrial and aquatic niches where plant and/or algal cellulosic cell walls are present. The microbial expansin phylogeny shows evidence of multiple horizontal gene transfer events within and between bacterial and eukaryotic microbial lineages, which may in part underlie their unusually broad phylogenetic distribution. Overall, expansins are unexpectedly widespread in bacteria and eukaryotes, and the contribution of these genes to microbial ecological interactions with plants and algae has probbaly been underappreciated.