Chitinolytic bacteria and chitin mineralization in the marine waters and sediments along the Antartic Peninsula

Abstract Chitinolytic bacteria were enumerated and isolated from marine waters and sediments along the highly productive Antarctic Peninsula. Chitinolytic bacteria were found in low concentrations (approximately 1 cell per ml) in the water column and at much higher levels in marine surface sediments (10⁴–10⁵ per g). The predominant chitinolytic bacteria isolated from the water column were identified as psychrophilic Vibrio spp. Rates of chitin mineralization were measured by collection of ¹⁴CO₂ respired from ¹⁴C-labeled chitin synthesized from chitosan and [1-¹⁴C]acetic anhydride. Chitin mineralization rates were extremely low in the marine waters analyzed (0.00085–0.0019% of the added label respired in 48 h) and appreciably higher in the marine sediments (0.0039–0.01% per 48 h), suggesting that the sediments are much more important in chitin degradation. Such low mineralization rates suggest that chitin may be accumulating in Antarctic marine sediments, though animals may also play an important role in chitin degradation.     

Differentiation of chitinase-active and non-chitinase-active subpopulations of a marine bacterium during chitin degradation

The ability of marine bacteria to adhere to detrital particulate organic matter and rapidly switch on metabolic genes in an effort to reproduce is an important response for bacterial survival in the pelagic marine environment. The goal of this investigation was to evaluate the relationship between chitinolytic gene expression and extracellular chitinase activity in individual cells of the marine bacterium Pseudoalteromonas sp. strain S91 attached to solid chitin. A green fluorescent protein reporter gene under the control of the chiA promoter was used to evaluate chiA gene expression, and a precipitating enzyme-linked fluorescent probe, ELF-97-N-acetyl-beta-D-glucosaminide, was used to evaluate extracellular chitinase activity among cells in the bacterial population. Evaluation of chiA expression and ELF-97 crystal location at the single-cell level revealed two physiologically distinct subpopulations of S91 on the chitin surface: one that was chitinase active and remained associated with the surface and another that was non-chitinase active and released daughter cells into the bulk aqueous phase. It is hypothesized that the surface-associated, non-chitinase-active population is utilizing chitin degradation products that were released by the adjacent chitinase-active population for cell replication and dissemination into the bulk aqueous phase.     

Chitin degradation by Clostridium sp. strain 9.1 in mixed cultures with saccharolytic and sulfate-reducing bacteria

Abstract The fermentation of chitin was studied in pure and cocultures of the chitinolytic Clostridium strain 9.1 and various non-hydrolytic sugar-fermenting and sulfate-reducing bacteria. A 5- to 8-fold enhancement of the rate of chitin degradation was observed, which was not due to the alleviation of inhibition of the chitinolytic enzyme system by polymer hydrolysis products. This was concluded from the observation that rates of chitinolysis and fermentation were unaffected by the addition of N -acetylglucosamine (NAG) or NAG-oligomers to pure cultures of strain 9.1, and from the absence of an unequivocal relation between the ability of a secondary bacterium to consume potentially inhibitory hydrolysis products and its capacity to stimulate chitin degradation. The acceleration of chitin fermentation in the presence of sugar-fermenting bacteria was the result of a release by these secondary populations of growth factors essential to strain 9.1. These factors comprised a high molecular, thioredoxin-like compound responsible for enhanced chitinolytic activity [10], and various low molecular compounds necessary for optimal growth. The sulfate reducers (except Desulfovibrio sp. strain 20028) released primarily the high molecular growth factor in coculture with strain 9.1. NAG-fermenting bacteria consumed approximately 10% of the hydrolysis products, whereas species capable of utilizing both mono- and oligomeric sugars fermented at least 50% of the sugars produced by strain 9.1. Nevertheless, the rate of chitinolysis in these cocultures proceeded at very similar rates.
The observed interactions between Clostridium sp. strain 9.1 and the secondary populations are discussed in relation to the results from studies on mixed culture fermentations of cellulosic substrates reported in the literature.     

Mycophagous mites and their internal associated bacteria cooperate to digest chitin in soil

The greater bulk of soil nitrogen is immobilized in chitinous cell walls of fungi. Mycophagous soil mites participate in chitin decomposition and, hence, in the subsequent mobilization of nitrogen. The source of the chitinolytic enzymes was searched in this study. A multimethodical approach was designed for these studies. Histology, plating and identification of bacteria from mite homogenate and, finally, homogenate and bacterial treatment of the soil fungi were applied. Here the presence and activity of chitinolytic bacteria inside mycophagous mites are reported. These bacteria form an extraintestinal group within the mite’s body and pass their enzymes into the mite’s gut. Our results demonstrate that true mycophagous mites, defined by their ability to digest chitin (i.e. the fungal cell wall), achieve this through internal “cooperation” with chitinolytic bacteria that provide the necessary chitinolytic enzymes. The nitrogen from chitin is thus made available to other soil organisms and plants.     

Biodegradation of shrimp processing bio-waste and concomitant production of chitinase enzyme and N-acetyl-D-glucosamine by marine bacteria: production and process optimization

A total of 250 chitinolytic bacteria from 68 different marine samples were screened employing enrichment method that utilized native chitin as the sole carbon source. After thorough screening, five bacteria were selected as potential cultures and identified as; Stenotrophomonas sp. (CFR221?M), Vibrio sp. (CFR173?M), Phyllobacteriaceae sp. (CFR16?M), Bacillus badius (CFR198?M) and Bacillus sp. (CFR188?M). All five strains produced extracellular chitinase and GlcNAc in SSF using shrimp bio-waste. Scanning electron microscopy confirmed the ability of these marine bacteria to adsorb onto solid shrimp bio-waste and to degrade chitin microfibers. HPLC analysis of the SSF extract also confirmed presence of 36-65?% GlcNAc as a product of the degradation. The concomitant production of chitinase and GlcNAc by all five strains under SSF using shrimp bio-waste as the solid substrate was optimized by 'one factor at a time' approach. Among the strains, Vibrio sp. CFR173?M produced significantly higher yields of chitinase (4.8 U/g initial dry substrate) and GlcNAc (4.7?μmol/g initial dry substrate) as compared to other cultures tested. A statistically designed experiment was applied to evaluate the interaction of variables in the biodegradation of shrimp bio-waste and concomitant production of chitinase and GlcNAc by Vibrio sp. CFR173?M. Statistical optimization resulted in a twofold increase of chitinase, and a 9.1 fold increase of GlcNAc production. These results indicated the potential of chitinolytic marine bacteria for the reclamation of shrimp bio-waste, as well as the potential for economic production of chitinase and GlcNAc employing SSF using shrimp bio-waste as an ideal substrate.     

Interactions of bacteria with different mechanisms for chitin degradation result in the formation of a mixed-species biofilm

In this study, interactions between bacteria possessing either released or cell-associated enzymes for polymer degradation were investigated. For this, a co-culture of Aeromonas hydrophila strain AH-1N as an enzyme-releasing bacterium and of Flavobacterium sp. strain 4D9 as a bacterium with cell-associated enzymes was set up with chitin embedded into agarose beads to account for natural conditions, under which polymers are usually embedded in organic aggregates. In single cultures, strain AH-1N grew with embedded chitin, while strain 4D9 did not. In co-cultures, strain 4D9 grew and outcompeted strain AH-1N in the biofilm fraction. Experiments with cell-free culture supernatants containing the chitinolytic enzymes of strain AH-1N revealed that growth of strain 4D9 in the co-culture was based on intercepting N-acetylglucosamine from chitin degradation. For this, strain 4D9 had to actively integrate into the biofilm of strain AH-1N. This study shows that bacteria using different chitin degradation mechanisms can coexist by formation of a mixed-species biofilm.     

Multiple components and induction mechanism of the chitinolytic system of the hyperthermophilic archaeon <Emphasis Type="Italic">Thermococcus chitonophagus</Emphasis>

Thermococcus chitonophagus produces several, cellular and extracellular chitinolytic enzymes following induction with various types of chitin and chitin oligomers, as well as cellulose. Factors affecting the anaerobic culture of this archaeon, such as optimal temperature, agitation speed and type of chitin, were investigated. A series of chitinases, co-isolated with the major, cell membrane-associated endochitinase (Chi70), and a periplasmic chitobiase (Chi90) were subsequently isolated. In addition, a distinct chitinolytic activity was detected in the culture supernatant and partially purified. This enzyme exhibited an apparent molecular mass of 50 kDa (Chi50) and was optimally active at 80°C and pH 6.0. Chi50 was classified as an exochitinase based on its ability to release chitobiose as the exclusive hydrolysis product of colloidal chitin. A multi-component enzymatic apparatus, consisting of an extracellular exochitinase (Chi50), a periplasmic chitobiase (Chi90) and at least one cell-membrane-anchored endochitinase (Chi70), seems to be sufficient for effective synergistic in vivo degradation of chitin. Induction with chitin stimulates the coordinated expression of a combination of chitinolytic enzymes exhibiting different specificities for polymeric chitin and its degradation products. Among all investigated potential inducers and nutrient substrates, colloidal chitin was the strongest inducer of chitinase synthesis, whereas the highest growth rate was obtained following the addition of yeast extract and/or peptone to the minimal, mineralic culture medium in the absence of chitin. In rich medium, chitin monomer acted as a repressor of total chitinolytic activity, indicating the presence of a negative feedback regulatory mechanism. Despite the undisputable fact that the multi-component chitinolytic system of this archaeon is strongly induced by chitin, it is clear that, even in the absence of any chitinous substrates, there is low-level, basal, constitutive production of chitinolytic enzymes, which can be attributed to the presence of traces of chito-oligosaccharides and other structurally related molecules (in the undefined, rich, non-inducing medium) that act as potential inducers of chitinolytic activity. The low, basal and constitutive levels of chitinase gene expression may be sufficient to initiate chitin degradation and to release soluble oligomers, which, in turn, induce chitinase synthesis.     

Physiological aspects of chitin catabolism in marine bacteria

Chitin, a carbohydrate polymer composed of alternating beta-1, 4-linked N-acetylglucosamine residues is the second most abundant organic compound in nature. In the aquatic biosphere alone, it is estimated that more than 10(11) metric tons of chitin are produced annually. If this enormous quantity of insoluble carbon and nitrogen was not converted to biologically useful material, the oceans would be depleted of these elements in a matter of decades. In fact, marine sediments contain only traces of chitin, and the turnover of the polysaccharide is attributed primarily to marine bacteria, but the overall process involves many steps, most of which remain to be elucidated. Marine bacteria possess complex signal transduction systems for: (1) finding chitin, (2) adhering to chitinaceous substrata, (3) degrading the chitin to oligosaccharides, (4) transporting the oligosaccharides to the cytoplasm, and (5) catabolizing the transport products to fructose-6-P, acetate and NH(3). The proteins and enzymes are located extracellularly, in the cell envelope, the periplasmic space, the inner membrane and the cytoplasm. In addition to these levels of complexity, the various components of these systems appear to be carefully coordinated by intricate regulatory mechanisms.     

Genomic analysis and initial characterization of the chitinolytic system of Microbulbifer degradans strain 2-40

The marine bacterium Microbulbifer degradans strain 2-40 produces at least 10 enzyme systems for degrading insoluble complex polysaccharides (ICP). The draft sequence of the 2-40 genome allowed a genome-wide analysis of the chitinolytic system of strain 2-40. The chitinolytic system includes three secreted chitin depolymerases (ChiA, ChiB, and ChiC), a secreted chitin-binding protein (CbpA), periplasmic chitooligosaccharide-modifying enzymes, putative sugar transporters, and a cluster of genes encoding cytoplasmic proteins involved in N-acetyl-D-glucosamine (GlcNAc) metabolism. Each chitin depolymerase was detected in culture supernatants of chitin-grown strain 2-40 and was active against chitin and glycol chitin. The chitin depolymerases also had a specific pattern of activity toward the chitin analogs 4-methylumbelliferyl-beta-D-N,N'-diacetylchitobioside (MUF-diNAG) and 4-methylumbelliferyl-beta-D-N,N',N"-triacetylchitotrioside (MUF-triNAG). The depolymerases were modular in nature and contained glycosyl hydrolase family 18 domains, chitin-binding domains, and polycystic kidney disease domains. ChiA and ChiB each possessed polyserine linkers of up to 32 consecutive serine residues. In addition, ChiB and CbpA contained glutamic acid-rich domains. At 1,271 amino acids, ChiB is the largest bacterial chitinase reported to date. A chitodextrinase (CdxA) with activity against chitooligosaccharides (degree of polymerization of 5 to 7) was identified. The activities of two apparent periplasmic (HexA and HexB) N-acetyl-beta-D-glucosaminidases and one cytoplasmic (HexC) N-acetyl-beta-D-glucosaminidase were demonstrated. Genes involved in GlcNAc metabolism, similar to those of the Escherichia coli K-12 NAG utilization operon, were identified. NagA from strain 2-40, a GlcNAc deacetylase, was shown to complement a nagA mutation in E. coli K-12. Except for the GlcNAc utilization cluster, genes for all other components of the chitinolytic system were dispersed throughout the genome. Further examination of this system may provide additional insight into the mechanisms by which marine bacteria degrade chitin and provide a basis for future research on the ICP-degrading systems of strain 2-40.     

Microbial synergists pathogenic to Lymantria dispar: Chitinolytic and fermentative bacterial interactions

A chitinolytic bacterium isolated from a healthy gypsy moth, Lymantria dispar, larva was shown to be pathogenic to larvae when administered per os after growth on chitin broth. However, the chitin hydrolase produced by this isolate had a pH optimum for activity of 5.5 and the high alkalinity in the mesenteron of L. dispar larvae severely limited chitinolysis of the midgut lining. Fermentative, nonpathogenic, acid-producing bacteria isolated from healthy gypsy moth larvae effectively lowered larval mesenteron pH when administered per os and the combination of fermentative isolates with a crude culture aliquot of the chitinolytic strain produced a synergistic increase in mortality over either dose administered by itself. Increased mortality was also observed for most fermentative strains when they were combined with crude supernatants of centrifuged cultures of the chitinolytic strain, although these combinations proved less effective than when fermenters were added to the whole-culture aliquots of the chitinolytic strain. In vitro studies showed that other bacteria isolated from environments foreign to that of the gypsy moth could ferment carbohydrates with acid production at an alkaline pH; however, in vivo studies demonstrated that these bacteria were incapable both of poising larval midgut pH and of enhancing mortality when added to chitinolytic bacteria.     

Chitinolytic enzymes and the bacterial microflora in the digestive tract of cod, Gadus morhua

The levels of chitinolytic enzymes and chitinolytic bacteria in the digestive tract of feeding and fasting cod were compared. Enzyme activities within a given tissue were of a similar order irrespective of the presence of chitinolytic bacteria and/or chitin. Cod chitinase and chitobiase are therefore endogenous and constitutive enzymes. Fasting cod had similar numbers of bacteria within the gastro-intestinal compartments as feeding fish. Representative bacterial isolates from fasting fish were characterized.     

Interspecies interaction based on transfer of a thioredoxin-like compound in anaerobic chitin-degrading mixed cultures

Abstract Fermentation of chitin by mixed cultures of the chitinolytic Clostridium sp. strain 9.1 and various non-chitinolytic bacteria proceeded up to eight times faster than in pure cultures. The addition of spent media of such mixed cultures also resulted in a marked stimulation of chitinolysis in pure cultures of strain 9.1. Pure cultures fermented chitin much faster if supplemented with either spent media or cell-free extracts of the non-chitinolytic bacteria. The compound responsible for this stimulation was thermostable (10 min at 85° C) and could not be removed by passage over Sephadex G-25, indicating a molecular weight of more than 1500. The heat stable enzyme thioredoxin (from Saccharomyces cerevisiae ) was shown to stimulate the chitin fermentation in a similar manner. Alkylation of this enzyme reduced its stimulatory action significantly indicating its (di)thiol: disulfide interchanging activity.
It is hypothesized that essential sulfhydryl groups in the chitinolytic system of strain 9.1 are reduced by thioredoxin and/or similar thiol: disulfide transhydrogenases present in the cell-free extracts and spent media, resulting in an acceleration of chitin hydrolysis and fermentation. This stimulation may thus be the result of a new type of interspecies interaction in anaerobic mixed cultures.     

Diversity of methyl halide-degrading microorganisms in oceanic and coastal waters

Methyl halides have a significant impact on atmospheric chemistry, particularly in the degradation of stratospheric ozone. Bacteria are known to contribute to the degradation of methyl halides in the oceans and marine bacteria capable of using methyl bromide and methyl chloride as sole carbon and energy source have been isolated. A genetic marker for microbial degradation of methyl bromide ( cmuA ) was used to examine the distribution and diversity of these organisms in the marine environment. Three novel marine clades of cmuA were identified in unamended seawater and in marine enrichment cultures degrading methyl halides. Two of these cmuA clades are not represented in extant bacteria, demonstrating the utility of this molecular marker in identifying uncultivated marine methyl halide-degrading bacteria. The detection of populations of marine bacteria containing cmuA genes suggests that marine bacteria employing the CmuA enzyme contribute to methyl halide cycling in the ocean.     

Chronological Events Associated with the Antagonistic Properties of Trichoderma harzianum against Botrytis cinerea: Indirect Evidence for Sequential Role of Antibiosis and Parasitism

Chronological events associated with the degradation of Botrytis cinerea by a strain of Trichoderma harzianum selected for superior biocontrol ability were studied using ultrastructure and cytochemical investigations in an attempt to define the relative roles of antibiosis and parasitism in the antagonistic process. The first ultrastructural changes were observed 12 h before contact between the organisms, and were characterized by punctuated invaginations of the Botrytis plasmalemma. These reactions were followed by a gradual retraction of the plasmalemma, disorganization of the cytoplasm, loss of turgor pressure and cell death within 48 h of contact between hyphae of the interacting fungi. The first evidence of penetration of B. cinerea by T. harzianum was recorded 72 h after contact. This penetration was apparently mediated by either mechanical pressure or localized wall digestion at points of entry, as there was no clear evidence of chitinolytic degradation of the B. cinerea cell wall, as determined by cytochemical labelling of chitin with a lectin-gold conjugate. However, after 10 days there was clear indication of chitin degradation, based on the random and reduced presence of gold particles over the cell wall of B. cinerea. These results suggest that the strain of T. harzianum antagonized first and foremost by antibiosis, leading to cell death, followed by degradation of the cell by means of chitinolytic enzymes. The production of antibiotics may, therefore, be more important than that of chitinolytic enzymes in conferring superior biocontrol properties to T. harzianum.     

Chitinolytic activity of bacteria

Chitinolytic bacteria play an important role in degradation of chitin, one of the most abundant biopolymers in nature. These microorganisms synthesize specific enzymes, that catalyze hydrolysis of beta-1,4-glycosidic bonds in low-digestible chitin polymers, turning it into low-molecular, easy to digest compounds. During last decades many bacterial chitinolytic enzymes have been studied and characterized, mainly for their potential applications in agriculture, industry and medicine. Several chitinase classifications have been proposed, either on the base of substrate specificity or amino acid sequence similarities. X-ray crystallography and NMR spectroscopy techniques enabled the determination of three dimensional structure of some chitinases, what was helpful in explaining their catalytic mechanism. Development of biotechnology and molecular biology enables a deep research in regulation and cloning of bacterial chitinase genes.     

Assessment of chitin decomposer diversity within an upland grassland

The breakdown of chitin within an acidic upland grassland was studied. The aim was to provide a molecular characterisation of microorganisms involved in chitin degradation in the soil using soil microcosms and buried litter bags containing chitin. The investigation involved an examination of the effects of liming on the microbial communities within the soil and their chitinolytic activity. Microcosm experiments were designed to study the influence of lime and chitin enrichment on the grassland soil bacterial community ex situ under controlled environmental conditions. Bacterial and actinomycete counts were determined and total community DNA was extracted from the microcosms and from chitin bags buried at the experimental site. PCR based on specific 16S rRNA target sequences provided products for DGGE analysis to determine the structure of bacterial and actinomycete communities. Chitinase activity was assessed spectrophotometrically using chitin labelled with remazol brilliant violet. Both liming and chitin amendment increased bacterial and actinomycete viable counts and the chitinase activity. DGGE band patterns confirmed changes in bacterial populations under the influence of both treatments. PCR products amplified from DNA isolated from chitin bags were cloned and sequenced. Only a few matched known species but a prominent coloniser of chitin proved to be Stenotrophomonas maltophilia.     

The novel method for isolating chitinolytic bacteria and its application in screening for hyperchitinase producing mutant of Alcaligenes xylosoxydans

AIMS: To develop a novel, rapid and effective screening method for chitinase producing bacteria. METHODS AND RESULTS: A simple and rapid technique for screening of potential chitinolytic bacteria has been developed using the chitin binding dye calcofluor white M2R in chitin agar. Microorganisms possessing high chitinolytic potential gave a clear zone under ultraviolet light after 24-48 h of incubation. This method was successfully applied for isolating the hyperchitinase mutant of Alcaligenes xylosoxydans. The mutant Alc. xylosoxydans EMS 33 was found to produce 3.4 times more chitinase than the wild type. CONCLUSIONS: In this study, the screening method for chitinase producing bacteria has been developed and it was applied to screen chitinase-overproducing mutant of Alc. xylosoxydans. SIGNIFICANCE AND IMPACT OF THE STUDY: The novel screening method for chitinase producer is more sensitive, rapid, user-friendly and reliable, which can also be used for screening of recombinants having chitinase gene.     

Chitinolytic activity of phylogenetically diverse Bacillus cereus sensu lato from natural environments

Bacillus cereus s.l., Gram-positive endospore-forming bacilli, persist ubiquitously in different natural habitats and play various ecological roles. Nevertheless, although chitin is one of the most abundant polymer on Earth, the study of the ability of B. cereus s.l. to hydrolyze this polymer were limited to individual B. cereus and B. thuringiensis strains only. Thus, to fill this gap in this research we focused on (i) the linkage between the capability to chitin degradation and the phylogenetic relatedness of B. cereus s.l. strains, and (ii) the genetic background of chitinolytic properties of these bacilli. Our results showed that chitin degradation is common among the B. cereus group members, yet strains clustered into particular phylogenetic groups differ in their chitinolytic capacity. Separate clustering of chitinolytic and non-chitinolytic strains in the phylogenetic tree indicates the ecotypic structure of these isolates. Two proteins belonging to subfamily A (ChiA) and subfamily B (ChiB) of the glycoside hydrolase GH18 family exhibited simultaneous chitobiosidase and endochitinase activities, and are responsible for chitin utilization by environmental B. cereus s.l. isolates.     

Degradation of barnacle nauplii: implications to chitin regulation in the marine environment

The exoskeleton of most invertebrate larval forms is made of chitin, which is a linear polysaccharide of β (1→4)-linked N-acetylglucosamine (GlcNAc) residues. These larval forms offer extensive body surface for bacterial attachment and colonization. In nature, degradation of chitin involves a cascade of processes brought about by chitinases produced by specific bacteria in the marine environment. Microbial decomposition of larval carcasses serves as an alternate mechanism for nutrient regeneration, elemental cycling and microbial production. The present study was undertaken to assess the influence of chitinase enzyme on the degradation of the nauplii of barnacle, Balanus amphitrite. The survival and abundance of bacteria during the degradation process under different experimental conditions was monitored. To the best of our knowledge, no such study is conducted to understand the degradation of larval exoskeleton using chitinase and its influence on bacteria. An increase in the chitinase activity with increase in temperature was observed. Scanning electron micrographs of chitinase treated nauplii showed scars on the surface of the barnacle nauplii initially and further disruption of the exoskeleton was observed with the increase in the treatment time. Bacterial abundance of the chitinase treated nauplii increased with the increase in enzyme concentration. Pathogenic bacteria such as Vibrio cholerae, V. alginolyticus, V. parahaemolyticus which were initially associated with the exoskeleton were absent after chitinase treatment, however, Bacillus spp. dominated subsequent to chitinase treatment and this might have important implications to marine ecosystem functioning.