Activating Biocake Communities Retards Jumps of Transmembrane Pressure in Membrane Bioreactors

Sudden jump of transmembrane pressure (TMP) in membrane bioreactors (MBRs), associated with abrupt aggravation of membrane fouling, limits practical applications of MBRs and calls for effective mitigation strategies. While the TMP jump is generally related to the bacterial activity of biocakes, the mechanisms underlying the TMP jump remain unclear. Herein, we conducted various backwash protocols with different nutrient (e.g., nitrate and sodium acetate) loadings on fouled membranes in MBRs to reveal the critical role of bacterial activity of biocakes for the TMP jump. The filtration tests showed a lower TMP jump rate for the membrane backwashed with a nutrient solution (a mixture of 180 mg/L NaNO3 and 200 mg/L NaAc, averaged at 1.40 kPa/d) than that backwashed with tap water (averaged at 3.56 kPa/d), implying that TMP jump could be efficiently mitigated by providing sufficient nutrients to biocake bacteria. The characterization of biocakes showed that high-nutrient solution backwash considerably increased bacterial viability and activity, while considerably reducing biomolecule accumulation on membranes. The keystone taxa (e.g., g_Aeromonas and o_Chitinophagaceae) in the network of nutrient-enriched biocake communities were involved in nitrate reduction and biomolecule degradation. Ecological null model analyses revealed that the deterministic manner mainly shaped biocake communities with high-nutrient availability. Overall, this study highlights the significance of the bacterial activity of biocakes for TMP development and provides potential alternatives for controlling membrane fouling.

Deciphering the bacterial microbiome in response to long-term mercury contaminated soil

Hg contaminated soils are of concern due to the toxic effects on soil microbes. Currently, the adaptation of bacterial community to long-term Hg contamination remains largely unknown. Here, we assessed the effects of Hg contaminated soils on the bacterial communities under controlled conditions using 16S rRNA gene amplicon sequencing. The results showed that the bacterial α-diversity and richness were significant positively correlated with total Hg (p < 0.05). Land-use type, pH, EC, TK, and nitrate-N played important roles in shaping the bacterial communities. Long-term Hg-contaminated soils can be divided into three types based on land use types: slag type, farmland type, and mining area type. The dominant phyla include Proteobacteria, Actinobacteriota, Acidobacteriota, Chloroflexi, and Firmicutes. The dominant genera identified were Pseudomonas, Gaiella, Sphingomonas, Bacillus, Arthrobacter, Nocardioides. Network analysis showed that dominant taxa had non-random co-occurrence patterns and module 1 had an important role in responding Hg stress. Keystone genera identified were Bauldia, Phycicoccus, Sphingomonas, Gaiella, Nitrospira. The above results further our understanding of the adaptation of the bacterial community in long-term Hg-contaminated soil. This study has important guiding significance for the use of bacterial consortia to remediate Hg-contaminated soil.

Effects of Essential Oils-Based Supplement and Salmonella Infection on Gene Expression, Blood Parameters, Cecal Microbiome, and Egg Production in Laying Hens

One of the main roles in poultry resistance to infections caused by Salmonella is attributed to host immunity and intestinal microbiota. We conducted an experiment that involved challenging Lohmann White laying hens with Salmonella Enteritidis (SE), feeding them a diet supplemented with an EOs-based phytobiotic Intebio^®. At 1 and 7 days post-inoculation, the expression profiles of eight genes related to immunity, transport of nutrients in the intestine, and metabolism were examined. Cecal microbiome composition and blood biochemical/immunological indices were also explored and egg production traits recorded. As a result, the SE challenge of laying hens and Intebio^® administration had either a suppressive or activating effect on the expression level of the studied genes (e.g., IL6 and BPIFB3), the latter echoing mammalian/human tissue-specific expression. There were also effects of the pathogen challenge and phytobiotic intake on the cecal microbiome profiles and blood biochemical/immunological parameters, including those reflecting the activity of the birds' immune systems (e.g., serum bactericidal activity, β-lysine content, and immunoglobulin levels). Significant differences between control and experimental subgroups in egg performance traits (i.e., egg weight/number/mass) were also found. The phytobiotic administration suggested a positive effect on the welfare and productivity of poultry.

Contrasting Patterns of the Bacterial Communities in Melting Ponds and Periglacial Rivers of the Zhuxi glacier in the Tibet Plateau

Since the early 21^st century, global climate change has been inducing rapid glacier retreat at an unprecedented rate. In this context, the melt ponds impart increasing unique footprints on the periglacial rivers due to their hydrodynamic connection. Given that bacterial communities control numerous ecosystem processes in the glacial ecosystem, exploring the fate of bacterial communities from melt ponds to periglacial rivers yields key knowledge of the biodiversity and biogeochemistry of glacial ecosystems. Here, we analyzed the bacterial community structure, diversity, and co-occurrence network to reveal the community organization in the Zhuxi glacier in the Tibet Plateau. The results showed that the bacterial communities in melt ponds were significantly lower in alpha-diversity but were significantly higher in beta-diversity than those in periglacial rivers. The rare sub-communities significantly contributed to the stability of the bacterial communities in both habitats. The co-occurrence network inferred that the mutually beneficial relationships predominated in the two networks. Nevertheless, the lower ratio of positive to negative edges in melt ponds than periglacial rivers implicated fiercer competition in the former habitat. Based on the significantly higher value of degree, betweenness, and modules, as well as shorter average path length in melt ponds, we speculated that their bacterial communities are less resilient than those of periglacial rivers.

The North Sea goes viral: Occurrence and distribution of North Sea bacteriophages

Marine viruses are dominated by phages and have an enormous influence on microbial population dynamics, due to lysis and horizontal gene transfer. The aim of this study is to analyze the occurrence and diversity of phages in the North Sea, considering the virus-host interactions and biogeographic factors. The virus community of four sampling stations were described using virus metagenomics (viromes). The results show that the virus community was not evenly distributed throughout the North Sea. The dominant phage members were identified as unclassified phage group, followed by Caudovirales order. Myoviridae was the dominant phage family in the North Sea, which occurrence decreased from the coast to the open sea. In contrast, the occurrence of Podoviridae increased and the occurrence of Siphoviridae was low throughout the North Sea. The occurrence of other groups such as Phycodnaviridae decreased from the coast to the open sea. The coastal virus community was genetically more diverse than the open sea community. The influence of riverine inflow and currents, for instance the English Channel flow affects the genetic virus diversity with the community carrying genes from a variety of metabolic pathways and other functions. The present study offers the first insights in the virus community in the North Sea using viromes and shows the variation in virus diversity and the genetic information moved from coastal to open sea areas.

Rare taxa and dark microbial matter: novel bioactive actinobacteria abound in Atacama Desert soils

An "in house" taxonomic approach to drug discovery led to the isolation of diverse actinobacteria from hyper-arid, extreme hyper-arid and very high altitude Atacama Desert soils. A high proportion of the isolates were assigned to novel taxa, with many showing activity in standard antimicrobial plug assays. The application of more advanced taxonomic and screening strategies showed that strains classified as novel species of Lentzea and Streptomyces synthesised new specialised metabolites thereby underpinning the premise that the extreme abiotic conditions in the Atacama Desert favour the development of a unique actinobacterial diversity which is the basis of novel chemistry. Complementary metagenomic analyses showed that the soils encompassed an astonishing degree of actinobacterial 'dark matter', while rank-abundance analyses showed them to be highly diverse habitats mainly composed of rare taxa that have not been recovered using culture-dependent methods. The implications of these pioneering studies on future bioprospecting campaigns are discussed.

Acclimation of Culturable Bacterial Communities under the Stresses of Different Organic Compounds

The phylogenetic diversity of bacterial communities in response to environmental disturbances such as organic pollution has been well studied, but little is known about the way in which organic contaminants influence the acclimation of functional bacteria. In the present study, tolerance assays for bacterial communities from the sediment in the Pearl River Estuary were conducted with the isolation of functional bacteria using pyrene and different estrogens as environmental stressors. Molecular ecological networks and phylogenetic trees were constructed using both 16S rRNA gene sequences of cultured bacterial strains and 16S rRNA gene-based pyrosequencing data to illustrate the successions of bacterial communities and their acclimations to the different organic compounds. A total of 111 bacterial strains exhibiting degradation and endurance capabilities in response to the pyrene estrogen-induced stress were successfully isolated and were mainly affiliated with three orders, Pseudomonadales, Vibrionales, and Rhodobacterales. Molecular ecological networks and phylogenetic trees showed various adaptive abilities of bacteria to the different organic compounds. For instance, some bacterial OTUs could be found only in particular organic compound-treated groups while some other OTUs could tolerate stresses from different organic compounds. Furthermore, the results indicated that some new phylotypes were emerged under stresses of different organic pollutions and these new phylotypes could adapt to the contaminated environments and contribute significantly to the microbial community shifts. Overall, this study demonstrated a crucial role of the community succession and the acclimation of functional bacteria in the adaptive responses to various environmental disturbances.

Exploring the Cultivable Ectocarpus Microbiome

Coastal areas form the major habitat of brown macroalgae, photosynthetic multicellular eukaryotes that have great ecological value and industrial potential. Macroalgal growth, development, and physiology are influenced by the microbial community they accommodate. Studying the algal microbiome should thus increase our fundamental understanding of algal biology and may help to improve culturing efforts. Currently, a freshwater strain of the brown macroalga Ectocarpus subulatus is being developed as a model organism for brown macroalgal physiology and algal microbiome studies. It can grow in high and low salinities depending on which microbes it hosts. However, the molecular mechanisms involved in this process are still unclear. Cultivation of Ectocarpus-associated bacteria is the first step toward the development of a model system for in vitro functional studies of brown macroalgal–bacterial interactions during abiotic stress. The main aim of the present study is thus to provide an extensive collection of cultivable E. subulatus-associated bacteria. To meet the variety of metabolic demands of Ectocarpus-associated bacteria, several isolation techniques were applied, i.e., direct plating and dilution-to-extinction cultivation techniques, each with chemically defined and undefined bacterial growth media. Algal tissue and algal growth media were directly used as inoculum, or they were pretreated with antibiotics, by filtration, or by digestion of algal cell walls. In total, 388 isolates were identified falling into 33 genera (46 distinct strains), of which Halomonas (Gammaproteobacteria), Bosea (Alphaproteobacteria), and Limnobacter (Betaproteobacteria) were the most abundant. Comparisons with 16S rRNA gene metabarcoding data showed that culturability in this study was remarkably high (∼50%), although several cultivable strains were not detected or only present in extremely low abundance in the libraries. These undetected bacteria could be considered as part of the rare biosphere and they may form the basis for the temporal changes in the Ectocarpus microbiome.

Rare symbionts may contribute to the resilience of coral-algal assemblages

The association between corals and photosynthetic dinoflagellates (Symbiodinium spp.) is the key to the success of reef ecosystems in highly oligotrophic environments, but it is also their Achilles‘ heel due to its vulnerability to local stressors and the effects of climate change. Research during the last two decades has shaped a view that coral host–Symbiodinium pairings are diverse, but largely exclusive. Deep sequencing has now revealed the existence of a rare diversity of cryptic Symbiodinium assemblages within the coral holobiont, in addition to one or a few abundant algal members. While the contribution of the most abundant resident Symbiodinium species to coral physiology is widely recognized, the significance of the rare and low abundant background Symbiodinium remains a matter of debate. In this study, we assessed how coral–Symbiodinium communities assemble and how rare and abundant components together constitute the Symbiodinium community by analyzing 892 coral samples comprising >110 000 unique Symbiodinium ITS2 marker gene sequences. Using network modeling, we show that host–Symbiodinium communities assemble in non-random ‘clusters‘ of abundant and rare symbionts. Symbiodinium community structure follows the same principles as bacterial communities, for which the functional significance of rare members (the ‘rare bacterial biosphere’) has long been recognized. Importantly, the inclusion of rare Symbiodinium taxa in robustness analyses revealed a significant contribution to the stability of the host–symbiont community overall. As such, it highlights the potential functions rare symbionts may provide to environmental resilience of the coral holobiont.

The Pelagic Bacterium Paraphotobacterium marinum Has the Smallest Complete Genome Within the Family Vibrionaceae

Members of the family Vibrionaceae are metabolically versatile and ubiquitous in natural environments, with extraordinary genome feature of two chromosomes. Here we reported the complete genome of Paraphotobacterium marinum NSCS20N07D^T, a recently described novel genus-level species in the family Vibrionaceae. It contained two circular chromosomes with a size of 2,593,992 bp with G+C content of 31.2 mol%, and a plasmid with a size of 5,539 bp. The larger chromosome (Chr. I) had a genome size of 1,426,504 bp with G+C content of 31.6 mol%, and the smaller one (Chr. II) had a genome size of 1,161,949 bp with G+C content of 30.8 mol%. The two chromosomes have strikingly similar G+C contents with difference of <1% and similar percentages of coding regions. Interestingly, by comparison to 134 species affiliated with seven genera within the family Vibrionaceae, P. marinum NSCS20N07D^T possessed the smallest genome size and lowest G+C content. Clusters of orthologous groups of proteins functional categories revealed that the two chromosomes had different distributions of functional classes, indicating they take different cellular functions. Surprisingly, Chr. II had a large proportion of unknown genes than Chr. I. Metabolic characteristics predicted that Chr. I performed the essential metabolism, which can be complemented by the Chr. II, such as amino acids biosynthesis. Microbial community analysis of in situ surface seawater revealed that P. marinum accounted for one to four sequences among more than 20,000 of 16S ribosomal RNA gene V4 contigs, representing it apparently appeared as a rare species. What’s more, P. marinum was anticipated to be specific to the pelagic ocean. This study will provide new insight into more understanding the genomic and metabolic features of multiple chromosomes in prokaryote and emphasize the ecological distribution of the members in the family Vibrionaceae as a rare species.

Actinobacterial Rare Biospheres and Dark Matter Revealed in Habitats of the Chilean Atacama Desert

The Atacama Desert is the most extreme non-polar biome on Earth, the core region of which is considered to represent the dry limit for life and to be an analogue for Martian soils. This study focused on actinobacteria because they are keystone species in terrestrial ecosystems and are acknowledged as an unrivalled source of bioactive compounds. Metagenomic analyses of hyper-arid and extreme hyper-arid soils in this desert revealed a remarkable degree of actinobacterial 'dark matter', evidenced by a detected increase of 34% in families against those that are validly published. Rank-abundance analyses indicated that these soils were high-diversity habitats and that the great majority of designated 'rare' genera (up to 60% of all phylotypes) were always rare. These studies have enabled a core actinobacterial microbiome common to both habitats to be defined. The great majority of detected taxa have not been recovered by culture dependent methods, neither, with very few exceptions, has their functional ecology been explored. A microbial seed bank of this magnitude has significance not just for Atacama soil ecosystem resilience but represents an enormous untapped resource for biotechnology discovery programmes in an era where resistance to existing antibiotics is rapidly becoming a major threat to global health.

Sustaining Rare Marine Microorganisms: Macroorganisms As Repositories and Dispersal Agents of Microbial Diversity

Recent analyses revealed that most of the biodiversity observed in marine microbial communities is represented by organisms with low abundance but, nonetheless essential for ecosystem dynamics and processes across both temporal and spatial scales. Surprisingly, few studies have considered the effect of macroorganism–microbe interactions on the ecology and distribution dynamics of rare microbial taxa. In this review, we synthesize several lines of evidence that these relationships cannot be neglected any longer. First, we provide empirical support that the microbiota of macroorganisms represents a significant part of marine bacterial biodiversity and that host-microbe interactions benefit to certain microbial populations which are part of the rare biosphere (i.e., opportunistic copiotrophic organisms). Second, we reveal the major role that macroorganisms may have on the dispersal and the geographic distribution of microbes. Third, we introduce an innovative and integrated view of the interactions between microbes and macroorganisms, namely sustaining the rares, which suggests that macroorganisms favor the maintenance of marine microbial diversity and are involved in the regulation of its richness and dynamics. Finally, we show how this hypothesis complements existing theories in microbial ecology and offers new perspectives about the importance of macroorganisms for the microbial biosphere, particularly the rare members.