Genomes of novel Myxococcota reveal severely curtailed machineries for predation and cellular differentiation

Cultured Myxococcota are predominantly aerobic soil inhabitants, characterized by their highly coordinated predation and cellular differentiation capacities. Little is currently known regarding yet-uncultured Myxococcota from anaerobic, non-soil habitats. We analyzed genomes representing one novel order (o__JAFGXQ01) and one novel family (f__JAFGIB01) in the Myxococcota from an anoxic freshwater spring (Zodletone spring) in Oklahoma, USA. Compared to their soil counterparts, anaerobic Myxococcota possess smaller genomes, and a smaller number of genes encoding biosynthetic gene clusters (BGCs), peptidases, one- and two-component signal transduction systems, and transcriptional regulators. Detailed analysis of thirteen distinct pathways/processes crucial to predation and cellular differentiation revealed severely curtailed machineries, with the notable absence of homologs for key transcription factors (e.g. FruA and MrpC), outer membrane exchange receptor (TraA), and the majority of sporulation-specific and A-motility-specific genes. Further, machine-learning approaches based on a set of 634 genes informative of social lifestyle predicted a non-social behavior for Zodletone Myxococcota. Metabolically, Zodletone Myxococcota genomes lacked aerobic respiratory capacities, but encoded genes suggestive of fermentation, dissimilatory nitrite reduction, and dissimilatory sulfate-reduction (in f_JAFGIB01) for energy acquisition. We propose that predation and cellular differentiation represent a niche adaptation strategy that evolved circa 500 Mya in response to the rise of soil as a distinct habitat on earth. Importance The Myxococcota is a phylogenetically coherent bacterial lineage that exhibits unique social traits. Cultured Myxococcota are predominantly aerobic soil-dwelling microorganisms that are capable of predation and fruiting body formation. However, multiple yet-uncultured lineages within the Myxococcota have been encountered in a wide range of non-soil, predominantly anaerobic habitats; and the metabolic capabilities, physiological preferences, and capacity of social behavior of such lineages remain unclear. Here, we analyzed genomes recovered from a metagenomic analysis of an anoxic freshwater spring in Oklahoma, USA that represent novel, yet-uncultured, orders and families in the Myxococcota. The genomes appear to lack the characteristic hallmarks for social behavior encountered in Myxococcota genomes, and displayed a significantly smaller genome size and a smaller number of genes encoding biosynthetic gene clusters, peptidases, signal transduction systems, and transcriptional regulators. Such perceived lack of social capacity was confirmed through detailed comparative genomic analysis of thirteen pathways associated with Myxococcota social behavior, as well as the implementation of machine learning approaches to predict social behavior based on genome composition. Metabolically, these novel Myxococcota are predicted to be strict anaerobes, utilizing fermentation, nitrate reduction, and dissimilarity sulfate reduction for energy acquisition. Our results highlight the broad patterns of metabolic diversity within the yet-uncultured Myxococcota and suggest that the evolution of predation and fruiting body formation in the Myxococcota has occurred in response to soil formation as a distinct habitat on earth.

Genomes of novel Myxococcota reveal severely curtailed machineries for predation and cellular differentiation

Cultured Myxococcota are predominantly aerobic soil inhabitants, characterized by their highly coordinated predation and cellular differentiation capacities. Little is currently known regarding yet-uncultured Myxococcota from anaerobic, non-soil habitats. We analyzed genomes representing one novel order (o__JAFGXQ01) and one novel family (f__JAFGIB01) in the Myxococcota from an anoxic freshwater spring in Oklahoma, USA. Compared to their soil counterparts, anaerobic Myxococcota possess smaller genomes, and a smaller number of genes encoding biosynthetic gene clusters (BGCs), peptidases, one- and two-component signal transduction systems, and transcriptional regulators. Detailed analysis of thirteen distinct pathways/processes crucial to predation and cellular differentiation revealed severely curtailed machineries, with the notable absence of homologs for key transcription factors (e.g. FruA and MrpC), outer membrane exchange receptor (TraA), and the majority of sporulation-specific and A-motility-specific genes. Further, machine-learning approaches based on a set of 634 genes informative of social lifestyle predicted a non-social behavior for Zodletone Myxococcota. Metabolically, Zodletone Myxococcota genomes lacked aerobic respiratory capacities, but encoded genes suggestive of fermentation, dissimilatory nitrite reduction, and dissimilatory sulfate-reduction (in f_JAFGIB01) for energy acquisition. We propose that predation and cellular differentiation represent a niche adaptation strategy that evolved circa 500 Mya in response to the rise of soil as a distinct habitat on earth.

The influence of benthic diatoms on the textures of carbonate-coated grains from a fluvial tufa spring in northern California

ABSTRACT Diatoms are common in terrestrial freshwater carbonate environments, but their influence on the resulting carbonate texture and porosity remains unquantified. This study investigates the effect of diatoms on the textural variability and syndepositional porosity of spring-associated carbonate coated grains from a freshwater spring in Henry Cowell State Park, northern California, USA. Carbonate coated grains (n = 60) were collected from the distal-most pool of the spring (∼ 300 m from the spring source) and the porosity of the 1 cm diameter fraction (n = 20) was determined using the ImageJ software by adjusting the threshold size for pores > 1000 μm2. Results reveal a strong positive correlation between the number of pores and the number of diatoms examined in each coated grain (r = 0.77). There is a moderate positive relationship between the length of the largest diatom and the minor-axis diameter of a best-fit ellipse of its corresponding pore (r = 0.60). The total pore area for pores associated with at least one diatom was significantly greater than the total pore area of pores that did not enclose diatom frustules (t = 1.80, p < 0.05). Textural observations show that fine-grained laminated textures contain fewer diatoms than the porous textures, suggesting that diatoms disrupt lamination continuity by introducing pore space. These findings have implications for the influence of diatoms on the syndepositional porosity of carbonate rocks from the Cretaceous to Recent and may help explain textural differences between modern marine carbonate microbialites and their Precambrian counterparts.

Temperature and predator cues interactively affect ontogenetic metabolic scaling of aquatic amphipods

A common belief is that body mass scaling of metabolic rate results chiefly from intrinsic body-design constraints. However, several studies have shown that multiple ecological factors affect metabolic scaling. The mechanistic basis of these effects is largely unknown. Here, we explore whether abiotic and biotic environmental factors have interactive effects on metabolic scaling. To address this question, we studied the simultaneous effects of temperature and predator cues on the ontogenetic metabolic scaling of amphipod crustaceans inhabiting two different aquatic ecosystems, a freshwater spring and a saltwater lagoon. We assessed effects of phenotypic plasticity on metabolic scaling by exposing amphipods in the laboratory to water with and without fish cues at multiple temperatures. Temperature interacts significantly with predator cues to affect metabolic scaling. Our results suggest that metabolic scaling is highly malleable in response to short-term acclimation. The interactive effects of temperature and predators show the importance of studying effects of global warming in realistic ecological contexts.

Abiotic drivers of protein abundance variation among natural populations

Identifying when and where environmental change induces molecular responses in natural populations is an important goal in contemporary ecology. It can aid in identifying molecular signatures of populations experiencing stressful conditions and potentially inform if species are approaching the limits of their tolerance niches. Achieving this goal is hampered by our limited understanding of the influence of environmental variation on the molecular systems of most ecologically relevant species as the pathways underlying fitness-affecting plastic responses have primarily been studied in model organisms under controlled laboratory conditions. In this study, we establish relationships between protein abundance patterns and the abiotic environment by profiling the proteomes of 24 natural populations of the caddisfly Crunoecia irrorata. We subsequently relate these profiles to natural variations in the abiotic characteristics of their freshwater spring habitats which shows that protein abundances and networks respond to abiotic variation according to the functional roles these proteins have. We provide evidence that geographic and past and present environmental differences between sites affect protein abundances and identifications, and that baseline reaction norms are ubiquitous and can be used as information rather than noise in comparative field studies. Taking this natural variation into account is a prerequisite if we are to identify the effects environmental change has on natural populations.