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The increasing use and discharge of nanoparticles (NPs) pose risks to microorganisms that maintain the health of aquatic ecosystems. Although NPs are toxic to microorganisms, they tend to form microbial aggregates to protect themselves. Two main mechanisms account for the reduced toxicity: the dense physical structure acts as a barrier to NP exposure in the interior of the aggregate, and aggregation stabilizes a complex microbial ecosystem that enhances the ability of the community to adapt to prolonged NP exposure. We highlight the opportunities and challenges for managing microbial aggregates in wastewater treatment to remove or control NPs. For example, understanding the resistance mechanisms can help to design smart NPs that are less toxic to useful microorganisms or more toxic towards pathogenic microorganisms. NPs inevitably enter aquatic ecosystems – natural and engineered – owing to their massive use and rapid growth trend in industry and commerce. NPs come into contact with microbial aggregates, which are ubiquitous in aquatic environments. NPs exert well-known toxicities to microorganisms but, compared to planktonic cells, microorganisms in microbial aggregates are much more able to protect themselves against NPs toxicity. The dense physical structure of the aggregates acts as a barrier to NP exposure in the interior of the aggregate. Aggregation also stabilizes microbial diversity and interactions, which enhance the ability of the community to adapt to prolonged NP exposure. Because microbial aggregates are relatively good at resisting NP toxicity, their already common use in the treatment of wastewaters becomes even more beneficial when the wastewater contains NPs.

The increasing use and associated loss of phosphorus to the environment pose risks to aquatic ecosystems. Technology for phosphorus removal based on microbial aggregates is a natural, ecologically widespread, and sustainable reclamation strategy. Two main processes dominate phosphorus removal by microbial aggregates: extra- and intra-cellular entrapment. Extracellular phosphorus entrapment relies on extracellular polymeric substances, while intracellular entrapment uses a wider variety of phosphorus-entrapping mechanisms. In microbial aggregates, microalgae–bacteria interactions, quorum sensing, and acclimation can enhance phosphorus removal. Based on these insights, we propose novel avenues for entrapping phosphorus using ecological and genetic engineering, manipulated interactions, and integrated processes to create phosphorus removal technology mediated by microbial aggregates. Phosphorus (P) entrapment by microbial aggregates is a natural process that requires relatively small amounts of operational inputs and is eco-friendly; it offers an effective means to remove P from eutrophic surface waters.Extracellular polymeric substances in microbial aggregates play an important role in extracellular P entrapment due to their inherent characteristics, chemical composition, and role in aggregation.Multiple mechanisms allow intracellular P entrapment by microalgae and polyphosphate-accumulating microorganisms in microbial aggregates.In microbial aggregates, microalgae–bacteria interactions, quorum sensing, and adaption can enhance the community’s ability to remove P.Ecological and genetic engineering, regulation of interactions, and integrated processes (microbial aggregates with enhanced biological P removal and bioelectrochemical system), can help to design P removal technology based on microbial aggregates.

In Europe, several gypsum karst regions occur among which the gypsum karsts located in Emilia-Romagna (UNESCO World Heritage Site since 2023) and Sicily are notable. The sediments, spring water microbial aggregates, and wall biofilms from three caves, Re Tiberio, Befana (Emilia-Romagna), and the Sicilian Santa Ninfa, have been studied from a microbiological and geochemical point of view. The samples of wall biofilms from gypsum caves were exclusively composed of Bacteria , while the sediments showed negligible abundances of Archaea . The two most abundant phyla in most sediments and biofilms were Actinomycetota and Pseudomonadota , whereas the microbial aggregates floating in the spring waters of Befana Cave showed a deviation from the typical abundance pattern as Campylobacterota replaced Actinomycetota , and the abundances of Bacteroidota and Desulfobacterota were high. The most abundant genus in the wall biofilms was Crossiella ( Actinomycetota ), but it was absent in the water aggregates collected in Befana Cave. The abundances of Crossiella in the cave sediments were very low. The dominant genera in Befana microbial aggregates showed different abundances and microbial composition when compared with the previously studied Frasassi and Fetida thermal sulfuric acid caves, located in Central and South Italy, respectively, suggesting that the community composition of the microbial aggregates is specific for each cave and related to the geochemistry of the sulfidic spring. Also, a different microbial community composition was found in Befana water aggregates with respect to the wall biofilms from Befana and Santa Ninfa caves. In the case of sediments, they significantly clustered together indicating that the microbial communities associated with sediments are similar, independently from the cave and possible other environmental parameters.

Granules in anammox reactors contain besides anammox bacteria other microbial communities whose identity and relationship with the anammox bacteria are not well understood. High calcium concentrations are often supplied to anammox reactors to obtain sufficient bacterial aggregation and biomass retention. The aim of this study was to provide the first characterization of bacterial and archaeal communities in anammox granules from a full-scale anammox reactor and to explore on the possible role of calcium in such aggregates. High magnification imaging using backscattered electrons revealed that anammox bacteria may be embedded in calcium phosphate precipitates. Pyrosequencing of 16S rRNA gene fragments showed, besides anammox bacteria (Brocadiacea, 32 %), substantial numbers of heterotrophic bacteria Ignavibacteriacea (18 %) and Anaerolinea (7 %) along with heterotrophic denitrifiers Rhodocyclacea (9 %), Comamonadacea (3 %), and Shewanellacea (3 %) in the granules. It is hypothesized that these bacteria may form a network in which heterotrophic denitrifiers cooperate to achieve a well-functioning denitrification system as they can utilize the nitrate intrinsically produced by the anammox reaction. This network may provide a niche for the proliferation of archaea. Hydrogenotrophic methananogens, which scavenge the key fermentation product H2, were the most abundant archaea detected. Cells resembling the polygon-shaped denitrifying methanotroph Candidatus Methylomirabilis oxyfera were observed by electron microscopy. It is hypothesized that the anammox process in a full-scale reactor triggers various reactions overall leading to efficient denitrification and a sink of carbon as biomass in anammox granules.

Oral biofilms develop under a range of different conditions and different environments. This review will discuss emerging concepts in microbial ecology and how they relate to oral biofilm development and the treatment of oral diseases. Clues to how oral biofilms develop may lie in other complex systems, such as interactions between host and gut microbiota, and even in factors that affect biofilm development on leaf surfaces. Most of the conditions under which oral biofilms develop are tightly linked to the overall health and biology of the host. Advances in molecular techniques have led to a greater appreciation of the diversity of human microbiota, the extent of interactions with the human host, and how that relates to inter-individual variation. As a consequence, plaque development may no longer be thought of as a generic process, but rather as a highly individualized process, which has ramifications for the treatment of the diseases it causes.

Oligosaccharides produced from the extracellular hydrolysis of biological materials can act as common goods that promote cooperative growth in microbial populations, whereby cell–cell aggregation increases both the per capita availability of resources and the per-cell growth rate. However, aggregation can also have detrimental consequences for growth, as gradients form within aggregates limiting the resource accessibility. We built a computational model, which predicts cooperation is restricted in dense cell aggregates larger than 10 µm because of the emergence of polymer and oligomer counter gradients. We compared these predictions to experiments performed with two well-studied alginate-degrading strains of Vibrio splendidus , which varied in their ability to secrete alginate lyase. We observed that both strains can form large aggregates (less than 50 µm), overcoming diffusion limitation by rearranging their internal structure. The stronger enzyme producer grew non-cooperatively and formed aggregates with internal channels that allowed exchange between the bulk environment and the aggregate, whereas the weak enzyme producer showed strongly cooperative growth and formed dense aggregates in which cells near the core mixed by active swimming. Our simulations suggest that the mixing and channelling reduce diffusion limitation and allow cells to uniformly grow in aggregates. Together, these data demonstrate that bacterial behaviour can help overcome competition imposed by resource gradients within cell aggregates. This article is part of a discussion meeting issue ‘Single cell ecology’.

Coral reefs are highly diverse ecosystems where symbioses play a pivotal role. Corals contain cell-associated microbial aggregates (CAMA), yet little is known about how widespread they are among coral species or the nature of the symbio tic relationship. Using histology, we found CAMA within 24 species of corals from 6 genera from Hawaii, American Samoa, Palmyra, Johnston Atoll, Guam, and Australia. Prevalence (%) of infection varied among coral genera: Acropora, Porites, and Pocillopora were commonly infected whereas Montipora were not. Acropora from the Western Pacific were significantly more likely to be infected with CAMA than those from the Central Pacific, whereas the reverse was true for Porites. Compared with apparently healthy colonies, tissues from diseased colonies were significantly more likely to have both surface and basal body walls infected. The close association of CAMA with host cells in numerous species of apparently healthy corals and lack of associated cell pathology reveals an intimate agent–host association. Furthermore, CAMA are Gram negative and in some corals may be related to chla mydia or rickettsia. We propose that CAMA in adult corals are facultative secondary symbionts that could play an important ecological role in some dominant coral genera in the Indo-Pacific. CAMA are important in the life histories of other animals, and more work is needed to understand their role in the dis tribution, evolution, physiology, and immunology of reef corals.

Microbial life is a key driver of global biogeochemical cycles. Similar to the distribution of humans on Earth, they are often not homogeneously distributed in nature but occur in dense clusters that resemble microbial cities. Within and around these clusters, diffusion is often assumed as the sole mass-transfer process that dictates nutrient supply and waste removal. In many natural and engineered systems such as biofilms in aquatic environments, aggregates in bioremediation, or flocs in wastewater treatment plants, these clusters are exposed to flow that elevates mass transfer, a process that is often overlooked. In this study, we show that advective fluxes can increase the local growth of bacteria in a single microenvironment by up to 50% and shape their metabolism by disrupting localized anoxia or supplying nutrients at different rates. Collectively, advection-enhanced mass transport may thus regulate important biogeochemical transformations in both natural and engineered environments.

Bacteria associated with plants have been observed frequently to form assemblages referred to as aggregates, microcolonies, symplasmata, or biofilms on leaves and on root surfaces and within intercellular spaces of plant tissues. In a wide range of habitats, biofilms are purported to be microniches of conditions markedly different from those of the ambient environment and drive microbial cells to effect functions not possible alone or outside of biofilms. This review constructs a portrait of how biofilms associated with leaves, roots and within intercellular spaces influence the ecology of the bacteria they harbor and the relationship of bacteria with plants. We also consider how biofilms may enhance airborne dissemination, ubiquity and diversification of plant-associated bacteria and may influence strategies for biological control of plant disease and for assuring food safety. Trapped by a nexus, coordinates uncertain Ever expanding or contracting Cannibalistic and scavenging sorties Excavations through signs of past alliances Consensus signals sound revelry Then time warped by viscosity Genomes showing codependence A virtual microbial beach party With no curfew and no time-out A few estranged cells seeking exit options, Looking for another menagerie. David Sands, Montana State University, Bozeman, February 2003

Vast quantities of oil-associated marine snow (MOS) formed in the water column as part of the natural biological response to the Deepwater Horizon drilling accident. Despite the scale of the event, uncertainty remains about the mechanisms controlling MOS formation and its impact on the environment. Following oil spills in aquatic environments, oil-associated flocculants observed within contaminated waters ultimately lead to the sedimentation of oil as marine oil snow (MOS). To better understand the role of aggregates in hydrocarbon degradation and transport, we experimentally produced a MOS sedimentation event using Gulf of Mexico coastal waters amended with oil or oil plus dispersant. In addition to the formation of MOS, smaller micrometer-scale (10- to 150-μm) microbial aggregates were observed. Visual inspection of these microaggregates revealed that they were most abundant in the oil-amended treatments and frequently associated with oil droplets, linking their formation to the presence of oil. The peak abundance of the microaggregates coincided with the maximum rates of biological hydrocarbon oxidation estimated by the mineralization of 14 C-labeled hexadecane and naphthalene. To elucidate the potential of microaggregates to serve as hot spots for hydrocarbon degradation, we characterized the free-living and aggregate-associated microbial assemblages using 16S rRNA gene sequencing. The microaggregate population was found to be bacterially dominated and enriched with putative hydrocarbon-degrading taxa. Direct observation of some of these taxa using catalyzed reporter deposition fluorescence in situ hybridization confirmed their greater abundance within microaggregates relative to the surrounding seawater. Metagenomic sequencing of these bacteria-oil microaggregates (BOMAs) further supported their community’s capacity to utilize a wide variety of hydrocarbon compounds. Taken together, these data highlight that BOMAs are inherent features in the biological response to oil spills and likely important hot spots for hydrocarbon oxidation in the ocean. IMPORTANCE Vast quantities of oil-associated marine snow (MOS) formed in the water column as part of the natural biological response to the Deepwater Horizon drilling accident. Despite the scale of the event, uncertainty remains about the mechanisms controlling MOS formation and its impact on the environment. In addition to MOS, we observed micrometer-scale (10- to 150-μm) aggregates whose abundance coincided with maximum rates of hydrocarbon degradation and whose composition was dominated by hydrocarbon-degrading bacteria with the genetic potential to metabolize a range of these compounds. This targeted study examining the role of these bacteria-oil microaggregates in hydrocarbon degradation reveals details of this fundamental component of the biological response to oil spills, and with it, alterations to biogeochemical cycling in the ocean.