Summary Rhizomicrobiome, the communities of microorganisms surrounding the root of the plant, plays a vital role in promoting plant growth and health. The composition of rhizomicrobiome is dynamic both temporally and spatially, and is influenced greatly by the plant host and environmental factors. One of the key influencing factors is rhizodeposits, composed of root‐released tissue cells, exudates, lysates, volatile compounds, etc. Rhizodeposits are rich in carbon and nitrogen elements, and able to select and fuel the growth of rhizomicrobiome. In this minireview, we overview the generation, composition and dynamics of rhizodeposits, and discuss recent work describing the general and specific impacts of rhizodeposits on rhizomicrobiome. We focus further on root exudates, the most dynamic component of rhizodeposits, and review recent progresses about the influence of specific root exudates in promoting bacterial root colonization, inducing biofilm development, acting as plant defence and shaping the rhizomicrobiome.

Protein lysine acetylation is a post-translational modification that alters the charge, conformation, and stability of proteins. A number of genome-wide characterizations of lysine-acetylated proteins, or acetylomes, in bacteria have demonstrated that lysine acetylation occurs on proteins with a wide diversity of functions, including central metabolism, transcription, chemotaxis, and cell size regulation. Bacillus subtilis is a model organism for studies of sporulation, motility, cell signaling, and multicellular development (or biofilm formation). In this work, we investigated the role of global protein lysine acetylation in multicellular development in B. subtilis. We analyzed the B. subtilis acetylome under biofilm-inducing conditions and identified acetylated proteins involved in multicellularity, specifically, swarming and biofilm formation. We constructed various single and double mutants of genes known to encode enzymes involved in global protein lysine acetylation in B. subtilis. Some of those mutants showed a defect in swarming motility while others demonstrated altered biofilm phenotypes. Lastly, we picked two acetylated proteins known to be important for biofilm formation, YmcA (also known as RicA), a regulatory protein critical for biofilm induction, and GtaB, an UTP-glucose-1-phosphate uridylyltransferase that synthesizes a nucleotide sugar precursor for biosynthesis of exopolysaccharide, a key biofilm matrix component. We performed site-directed mutagenesis on the acetylated lysine codons in ymcA and gtaB, respectively, and assayed cells bearing those point mutants for biofilm formation. The mutant alleles of ymcA(K64R), gtaB(K89R), and gtaB(K191R) all demonstrated a severe biofilm defect. These results indicate the importance of acetylated lysine residues in both YmcA and GtaB. In summary, we propose that protein lysine acetylation plays a global regulatory role in B. subtilis multicellularity.

9Acinetobacter baumannii, a Gram-negative opportunistic pathogen, is a leading cause of hospital-10 acquired infections. A. baumannii is difficult to eradicate from hospitals due to its propensity to 11 quickly gain antibiotic resistances and ability to robustly survive on dry surfaces. These strategies are 12 largely mediated by mutagenesis and biofilm development, respectively. Mutagenesis is partly 13 governed by the DNA damage response (DDR). Biofilms are multicellular communities, often 14 surface-attached, that are more difficult to eradicate than free-living planktonic cells. There is 15 increasing evidence that the DDR and biofilm development are linked processes. Here, we show that 16 upon DNA damage, the relative intracellular concentration of RecA, the key DDR protein, is lower 17 than those of Escherichia coli. Notably, we report that RecA negatively influences biofilm 18 development. Cells lacking RecA (∆recA), that are unable to upregulate the DDR, have increased 19 surface attachment and sugar content within the biofilm matrix. We further show that in A. 20 baumannii, a modest increase in RecA concentrations, akin to DDR induction, decreases surface-21 attachment. Importantly, biofilms formed by ∆ recA cells are more difficult to eradicate with 22 2 antibiotic treatment. The evidence suggests that the A. baumannii DDR influences survival 23 independent from mutagenesis. It also demonstrates the importance of understanding fundamental 24 biology to better appreciate the relationships between different bacterial survival strategies. 25 Introduction 26Acinetobacter baumannii is an emerging Gram-negative opportunistic pathogen and one of the 27 ESKAPE pathogens, a group of bacteria responsible for the majority of hospital-acquired infections 28 1 . Interest in these bacteria has stemmed from A. baumannii outbreaks in hospitals worldwide that are 29 difficult to eradicate, due to increased multi-drug resistance (MDR) 2 and resistance to desiccation 3 . 30A. baumannii is very dangerous to immunocompromised individuals, causing different illnesses, 31including pneumonia, septicemia, and wound infections 4 . 32One response pathway that underlies MDR is the DNA damage response (DDR). When gene 33 products involved in antibiotic binding or processing are mutated, resistance is acquired 5 . 34Mutagenesis can result from induction of error-prone DNA polymerase genes which are part of the 35 DDR regulon, a strategy used by different bacteria 6,7 . In Escherichia coli and many other bacteria, 36 the cells' main recombinase, RecA, and the global transcriptional repressor, LexA, manage the DDR, 37 also known as the SOS response 8 . In A. baumannii, however, there is no known LexA homologue, 38 making the A. baumannii DDR circuitry unique 9,10 . We have shown that in A. baumannii expression 39 of multiple error-prone polymerases and clinically-relevant antibiotic resistance acquisition are 40 dependent on RecA 11 . 41A. baumannii is notorious for its ability to robustly survive on surfaces. Under dry conditions, A....

Biofilm development in Bacillus subtilis is regulated at multiple levels. While a number of known signals that trigger biofilm formation do so through the activation of one or more sensory histidine kinases, it was discovered that biofilm activation is also coordinated by sensing intracellular metabolic signals, including serine starvation. Serine starvation causes ribosomes to pause on specific serine codons, leading to a decrease in the translation rate of sinR, which encodes a master repressor for biofilm matrix genes and ultimately triggers biofilm induction. How serine levels change in different growth stages, how B. subtilis regulates intracellular serine levels, and how serine starvation triggers ribosomes to pause on selective serine codons remain unknown. Here, we show that serine levels decrease as cells enter stationary phase and that unlike most other amino acid biosynthesis genes, expression of serine biosynthesis genes decreases upon the transition into stationary phase. The deletion of the gene for a serine deaminase responsible for converting serine to pyruvate led to a delay in biofilm formation, further supporting the idea that serine levels are a critical intracellular signal for biofilm activation. Finally, we show that levels of all five serine tRNA isoacceptors are decreased in stationary phase compared with exponential phase. However, the three isoacceptors recognizing UCN serine codons are reduced to a much greater extent than the two that recognize AGC and AGU serine codons. Our findings provide evidence for a link between serine homeostasis and biofilm development in B. subtilis. IMPORTANCE In Bacillus subtilis, biofilm formation is triggered in response to environmental and cellular signals. It was proposed that serine limitation acts as a proxy for nutrient status and triggers biofilm formation at the onset of biofilm entry through a novel signaling mechanism caused by global ribosome pausing on selective serine codons. In this study, we reveal that serine levels decrease at the biofilm entry due to catabolite control and a serine shunt mechanism. We also show that levels of five serine tRNA isoacceptors are differentially decreased in stationary phase compared with exponential phase; three isoacceptors recognizing UCN serine codons are reduced much more than the two recognizing AGC and AGU codons. This finding indicates a possible mechanism for selective ribosome pausing.

The Atacama Desert, the driest and oldest desert in the world, is a hostile environment for life. Despite the inhospitable conditions, bacterial sequences detected in this location suggest rich bacterial life. This study tested the idea that certain bacteria would thrive in this location and that some of them could be cultivated permitting further characterization. Environmental surface soil samples from 1-5 cm deep were collected from 18 diverse locations within the Atacama Desert. To assess the bacterial taxa, diversity, and abundance, Illumina 16S rRNA gene sequencing was performed directly on soil samples. Bacteria were also cultured from the samples. We have a collection of 74 unique bacterial isolates after cultivation and confirmation by 16S rRNA gene sequencing. Pigmentation, biofilm formation, antibiotic production against Escherichia coli MG1655 and Staphylococcus aureus HG003, and antibiotic resistance were assessed on these isolates. We found that approximately a third of the colonies produced pigments, 80% of isolates formed biofilms, many isolates had antibiotic activity against E. coli and/or S. aureus, and many were resistant to commercial antibiotics. The functional characterization of these isolates gives us insight into the adaptive bacterial strategies in harsh environments and enables us to learn about their possible use in agriculture, healthcare, or biotechnology.Originality-Significant StatementThis study provides the first microbial diversity analysis from Atacama Desert soil, presents the cultivation and isolation of 74 unique bacterial isolates, many of which may be novel genera and species, and explores pigment production, antibiotic production and resistance, and unique biofilm development as bacterial survival strategies for living within extreme environments.

25Biofilm development in Bacillus subtilis is regulated at multiple levels. While a number 26 of known signals that trigger biofilm formation do so through the activation of one or more 27 sensory histidine kinases, it was recently discovered that biofilm activation is also coordinated by 28 sensing intracellular metabolic signals, including serine starvation. Serine starvation causes 29 ribosomes to pause on specific serine codons, leading to a decrease in the translation rate of sinR, 30 which encodes a master repressor for biofilm matrix genes, and ultimately biofilm induction. 31 How serine levels change in different growth stages, how B. subtilis regulates intracellular serine 32 levels in response to metabolic status, and how serine starvation triggers ribosomes to pause on 33 selective serine codons remain unknown. Here we show that serine levels decrease as cells enter 34 stationary phase and that unlike most other amino acid biosynthesis genes, expression of serine 35 biosynthesis genes decreases upon the transition into stationary phase. Deletion of the gene for a 36 serine deaminase responsible for converting serine to pyruvate led to a delay in biofilm 37 formation, further supporting the idea that serine levels are a critical intracellular signal for 38 biofilm activation. Finally, we show that levels of all five serine tRNA isoacceptors are 39 decreased in stationary phase compared to exponential phase. Interestingly, the three 40 isoacceptors recognizing UCN serine codons are reduced to a much greater extent than the two 41 that recognize AGC and AGU serine codons. Our findings provide evidence for a link between 42 serine homeostasis and biofilm development in B. subtilis. 43 44 3 IMPORTANCE 45In Bacillus subtilis, biofilm formation is triggered in response to various environmental 46 and cellular signals. It was previously proposed that serine limitation acts as a proxy for nutrient 47 status and triggers biofilm formation at the onset of biofilm entry through a novel signaling 48 mechanism caused by global ribosome pausing on selective serine codons. In this study, we 49 revealed that serine levels decrease at the biofilm entry due to catabolite control and a shunt 50 mechanism. We also show that levels of five serine tRNA isoacceptors are differentially 51 decreased in stationary phase compared to exponential phase; three isoacceptors recognizing 52 UCN serine codons are reduced much greater than the two recognizing AGC and AGU codons. 53This indicates a possible mechanism for selective ribosome pausing. 54 55 4

Lysine acetylation is a post‐translational modification that alters the charge, conformation, and stability of proteins. Published lists of acetylated proteins, or acetylomes, in bacteria have demonstrated that lysine acetylation occurs on proteins with a wide diversity of function, including central metabolism, DNA transcription and binding, chemotaxis, and cell size. Bacillus subtilis is a non‐pathogenic soil bacterium, and model organism for sporulation, motility, biofilm formation, and general multicellular development. The genetic regulation of these processes has been extensively studied, thus, we aimed to investigate the role of lysine acetylation in multicellular development (or biofilm formation) in B. subtilis. To further investigate acetylation, we generated an acetylome under biofilm‐inducing conditions and identified acetylated proteins involved in multicellularity; specifically, swarming and biofilm formation. Upon deletion of known genes for acetylation, cells had significantly slower swarming kinetics and a significantly smaller final swarming radius compared to wildtype. This suggests that acetylation impacts bacterial swarming. Biofilm is a mixture of cells and secreted matrix consisting of exopolysaccharides, proteins, and nucleotides that assists bacterial communities in colonization and survival. Genetic analysis of acetylation in biofilm formation demonstrated that lack of acetylation impacts biofilm development as shown by a decrease in matrix production. Targeting the acetylated biofilm proteins, we performed site‐directed mutagenesis of known acetylated lysine residues and assayed for biofilm formation. Two biofilm proteins, YmcA, a biofilm regulatory protein, and GtaB, an enzyme for biosynthesis of a precursor sugar for exopolysaccharides, demonstrated severe biofilm defects upon mutation of lysine residues. This suggests the importance of YmcA Lys64 and GtaB Lys89 and Lys191 for function in biofilm formation. In summary, we believe that protein lysine acetylation is a novel regulatory mechanism linking cell metabolism to bacterial multicellular development.Support or Funding InformationNational Science Foundation and Northeastern UniversityThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Central carbon metabolism acts as a regulator of bacterial intracellular activity based on environmental conditions. Understanding the processes regulated by metabolism will provide insight into how bacteria grow and develop for applications in biotechnology and infectious disease. Acetyl‐Coenzyme A (acetyl‐CoA), a molecular intermediate of carbon metabolism, is essential for various cellular processes including energy production, cell development, and protein acetylation. The acetate pathway acts as a relief mechanism for excess carbon metabolism by converting acetyl‐CoA into acetate, which is secreted by the cell. Inactivation of the acetate pathway causes a buildup of acetyl‐CoA accompanied by delayed growth and cell death in Bacillus subtilis, a Gram‐positive soil dwelling bacterium commonly used as a model for molecular microbiology research. However, the mechanism behind these acetyl‐CoA‐mediated growth defects are unknown. The acetate pathway was inactivated in B. subtilis by knocking out the ackA gene (ΔackA). ΔackA suppressor mutants were isolated based on recovered growth, and morphology studies and whole genome sequencing were performed to investigate underlying pathways. ΔackA cells exhibited altered morphology, including elongated cells and blebbing, which indicated defects in cell division and cell wall biosynthesis. The suppressors, however, exhibited significantly recovered growth and morphology resembling wild type cells. Whole genome sequencing revealed that several suppressors had mutations in pyruvate dehydrogenase complex genes pdhA and pdhC, likely inhibiting production of excess acetyl‐CoA. An additional mutation was observed in dapH, a gene involved in the acetylation of a cell wall precursor. These results suggest that acetyl‐CoA levels act as a signaling mechanism to connect metabolic status to cell wall biosynthesis and that the cell maintains a balance of acetyl metabolites for proper growth. This study deepens our understanding of metabolism as a regulatory mechanism for cellular processes.