Home Journals Articles Updates About
CN
image
收藏切换
Phylogenetically diverse, acetaldehyde-degrading bacterial community in the deep sea water of the West Pacific Ocean
收藏切换
PDF
Boliang GAO1, †, Xiexie SHANG1, †, Li LI2, Wenjie DI2, Runying ZENG2, 3, *
Acta Oceanologica Sinica | 2018, 37(8) : 54 - 64
Less
收藏切换
Acta Oceanologica Sinica | 2018, 37(8): 54-64
• Marine Biology •
Phylogenetically diverse, acetaldehyde-degrading bacterial community in the deep sea water of the West Pacific Ocean
Full
Boliang GAO1, †, Xiexie SHANG1, †, Li LI2, Wenjie DI2, Runying ZENG2, 3, *
Affiliations
  • 1 School of Life Sciences, Xiamen University, Xiamen 361102, China
  • 2 State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, China
  • 3 Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen 361005, China
Published: 2018-08-25 doi: 10.1007/s13131-018-1235-z
Outline
收藏切换

As a major aldehyde pollutant widely existing in industry and our daily life, acetaldehyde is more and more harmful to human health. As characteristic habitat niche, bacteria from deep sea environments are abundant and distinctive in heredity, physiology and ecological functions. Thus, the development of acetaldehyde-degrading bacteria from deep sea provides a new method to harness acetaldehyde pollutant. Firstly, in this study, acetaldehyde-degrading bacteria in the deep sea water of the West Pacific Ocean were enriched in situ and in the laboratory respectively, and then the diversity of uncultured bacteria was studied by using 16S rRNA genes. Then acetaldehyde-degrading strains were isolated from two samples, including enrichment in situ and enrichment in laboratory samples of deep sea water from the West Pacific Ocean using acetaldehyde as the sole carbon source, and then the ability of acetaldehyde degradation was detected. Our results showed that the main uncultured bacteria of two samples with different enrichment approaches were similar, including Proteobacteria, Actinobacteria, Firmicutes, Cyanobacteria, but the structure of bacterial community were significant different. Four subgroups, α, γ, δ and ε, were found in Proteobacteria group. The γ-Proteobacteria was dominant (63.5% clones in laboratory enriched sample, 75% clones in situ enriched sample). The species belonged to γ-Proteobacteria and their proportion was nearly identical between the two enrichment samples, and Vibrio was the predominant genus (45% in laboratory enriched sample, 48.5% in situ enriched sample), followed by Halomonas (9% in situ enriched sample) and Streptococcus (6% in laboratory enriched sample). A total of 12 acetaldehyde-degrading strains were isolated from the two samples, which belonged to Vibrio, Halomonas, Pseudoalteromonas, Pseudomonas and Bacillus of γ-Proteobacteria. Strains ACH-L-5, ACH-L-8 and ACH-S-12, belonging to Vibrio and Halomonas, have strong ability of acetaldehyde degradation, which could tolerate 1.5 g/L acetaldehyde and degrade 350 mg/L acetaldehyde within 24 hours. Our results indicated that bacteria of γ-Proteobacteria may play an important role in carbon cycle of deep sea environments, especial the bacteria belonging to Vibrio and Halomonas and these strains was suggested for their potentials in government of aldehyde pollutants.

acetaldehyde-degrading bacteria  /  ALDH  /  deep sea  /  in situ
Boliang GAO, Xiexie SHANG, Li LI, Wenjie DI, Runying ZENG. Phylogenetically diverse, acetaldehyde-degrading bacterial community in the deep sea water of the West Pacific Ocean[J]. Acta Oceanologica Sinica, 2018 , 37 (8) : 54 -64 . DOI: 10.1007/s13131-018-1235-z
Full Text
Less
1 Introduction
Less
Deep sea is the biggest Gene Bank on the earth, which contains abundant marine microorganisms. Previous studies paid great attentions to the marine microorganisms in shallow sea, and many marine microorganisms have been reported (Okami et al., 1976; Okazaki et al, 1975; Ding and Valentine, 2008). Compared with a lot of research attentions on marine microorganisms in shallow sea, the investigation of marine microorganisms in deep sea is relatively lacking. Deep sea has extremely heavy climate and environment, for example strong acid and base, high or low temperature, high pressure. Therefore, marine microorganisms of deep sea are significantly different with microorganisms from land including genetic constitution, metabolism regulation, metabolite, chemical defense, and many microorganisms which are acidophilic, basophilic, haloduric and so on (Horikoshi, 1998; Ista et al., 2004; Koyama and Yoshida, 2016). The refractory organisms which come from upper layer of the ocean and bottom sediments are the main nutrient source of microorganisms in deep sea (Horikoshi, 1998; Gao et al., 2017). Thus the microorganisms in deep sea have potential of environment government, for example apply in industrial wastewater treatment. Meanwhile, the potential application of microorganisms of deep sea in biomedicine, new biomaterial was noticed. As exhaustion of land resources, the marine microorganisms, especially the microorganisms of deep sea will be one of spot for exploitation.
The pollutant of aldehydes widely exists in the environment, for example methanol, acetaldehyde, acraldehyde (Zhou et al., 2005; Gesser and Fu, 1990; Xi et al., 1999). Previous studies have reported that the superfluous acetaldehyde in furniture materials have been noticed by people, and that is harmful to humans (Homann et al., 2000). While acetaldehyde dangers have not been noticed yet by people. Acetaldehyde is toxic when applied externally for prolonged periods, an irritant, and a probable carcinogen. At present, enzymatic degradation by the acetaldehyde dehydrogenase is the main efficient way to degrade acetaldehyde (Lubin and Westerfield, 1945; Svegliati-Baroni et al., 2001). Unfortunately, the extraction of acetaldehyde dehydrogenase is costly and difficult. Furthermore, as the complex chemical constituents of acetaldehyde industrial wasted water, gas and residue, such as high heavy metal, strong acid and alkali, so the degradation of acetaldehyde by the acetaldehyde dehydrogenase is infeasible (van der Ploeg et al., 1994; Lachenmeier and Sohnius, 2008; Kurkivuori et al., 2007). To address this issue, recent studies have more focused on microbial catalyzing, especially the bacteria in deep sea.
Although technique of microbial pure culture which obtains microbial pure culture by isolation, purification, culture of microorganism has encountered un-overstepped obstacle for studying diversity of microorganism, it is irreplaceable for study of cellular structure, physiology, genetics and application of microorganism. To isolate microorganisms as far as possible, the technique of microbial pure culture was improved. New technique without high concentration of nutrients and manual preparation could provide primitive ecology for microorganisms, and the enrichment of microorganisms in situ is one of frequently used techniques. Kaeberlein et al. (2002) have obtained many more stains used this technique than traditional separation methods. Furthermore, molecular ecological techniques have recently been used to study bacterial diversity in situ (Kirk et al., 2004). This stems from the fact that many microorganisms are not easily obtainable as cultured strains in laboratory, which would allow for identification and characterization.
In this study, with the aim to know about the acetaldehyde-degrading bacterial phylogenetic diversity and to search strains with the potential application of acetaldehyde degradation in the deep sea water of the West Pacific Ocean, enrichment in situ and in the laboratory respectively, the uncultured and cultured bacterial phylogenetic diversity and the ability of acetaldehyde-degrading of bacteria in the deep sea water of the West Pacific Ocean were investigated. Besides, the potential application of acetaldehyde-degrading bacteria in the deep sea water of the West Pacific Ocean was suggested.
2 Materials and methods
Less
2.1 Sampling
Enrichment in laboratory: Deep sea water was sampled at the depth of 2 000 m in the West Pacific Ocean (21°03′30″N, 118°23′17″E) in September 2012. A total of 30 mL deep sea water was loaded in 50 mL reagent bottle with 5 g absorbing 40% acetaldehyde of active carbon, and the reagent bottle was stored in a cold storage (8°C) for 6 months.
Enrichment in situ: regent bottles were placed at the depth of 2 000 m in the West Pacific Ocean (21°03′30″N, 118°23′17″E) in September 2012. There were active carbon granules which absorbed 40% acetaldehyde in these regent bottles, and some pores were on these regent bottles for internal and external material exchange, and bacteria were enriched in situ for six months.
2.2 Total genomic DNA extraction, PCR amplification of 16S rRNA gene, and clone library structure
Total genomic DNA was extracted from two kinds of samples, respectively, using PowerSoil DNA Isolation Kit (MOBIO). The quality and concentration of the soil DNA were assessed using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, USA). The overall size of the total DNA was checked by running an aliquot of DNA on a 1.0% agarose gel, and then was stored in –20°C until further processing.
The resulting genomic DNA was used as templates to amplify the bacterial 16S rRNA gene fragment using common primers 27F and 1492R. The PCR mixture (50 μL) contained 2 μL DNA template, 5 μL 10×Taq buffer (Mg2+), 4 μL dNTP mixture (2.5 mmol/L), 1 μL of each primer (10 μmol/L), 0.5 μL EXTaq DNA polymerase (5 U/μL). The PCR program was carried out with 3 min at 95°C, followed by 30 cycles of denaturation at 95°C for 90 s, annealing at 55°C for 90 s and elongation at 72°C for 90 s, and final elongation at 72°C for 10 min. PCR products were purified using Gel Extraction Kit (Omega). PCR products were ligated into pTA-2 Vector and transformed into E. coli DH5α. PCR was performed to detect whether the picked clones were positive recombinants. Two different clone libraries were structured. A total of 200 positive clones were selected from each clone library and sequenced using primers T3 and T7 by Shanghai Majorbio Company.
2.3 16S rRNA genes phylogenetic diversity and bacterial diversity analysis
After removing the sequences of plasmid vector, 1 400–1 500 bp 16S rRNA genes were obtained in this study, and were checked chimera on the DECIPHER-Find Chimeras. These sequences were aligned on the Rdp Pipeline Tools to identify sequences similarity. Sequences with similarity not less than 97% were classified as one OTUs, while similarity less than 97% were classified different OTUs. The representative sequences were selected, and then phylogenetic trees based on gene sequences of 16S rRNA were constructed using neighbor-joining method in MEGA 5.0 combined with bootstrap analysis setting with 1 000 replications, respectively. Coverage estimator based on Coverage C (Chao and Lee, 1992) and species richness was assessed with Chao1 (Chao, 1984), while evenness and diversity of species were estimated by Evenness index (E′) and Shannon diversity index (H′) (Chao and Shen, 2003).
2.4 Isolation and identification of cultivable acetaldehyde-degrading bacteria
To further screen cultivable acetaldehyde-degrading bacteria, acetaldehyde was used as sole carbon source for the growth of acetaldehyde-degrading bacteria. Two different samples (5 g) were vortex shocked with 5 min, and then serial 10-fold dilutions (each sample in sterile sea water) were plated on the corresponding solid modified 2216E (0.1% yeast extract, 2% agar powder, 720 mg/L acetaldehyde and sea water) and incubated for 48 h at 37°C. Subsequently, individual bacteria were removed from agar plates, placed on new medium and checked for purity and stored in 20% glycerol at –80°C.
The genomic DNA of acetaldehyde-degrading bacteria was extracted using TaKaRa MiniBEST Bacteria Genomic DNA Extraction Kit Ver. 3.0. The resulting genomic DNA was used as templates to amplify the bacterial 16S rRNA gene fragment using common primers 27F and 1492R. PCR products were sequenced in Shanghai Majorbio Company after analysis by electrophoresis on 1.5% agarose gel. A total of 1 400–1 500 bp of Bacterial 16S rRNA genes sequences were obtained in this study and aligned on the NCBI database. The most appropriate relative sequences were selected and it can be sure genus or family of bacteria until the similarity not less than 99%.
2.5 Detection of acetaldehyde-degrading ability of cultivable acetaldehyde-degrading bacteria
To detect the tolerance of cultivable acetaldehyde-degrading bacteria toward acetaldehyde, bacterial cells were grown in 5 mL 2216E with different concentrations of acetaldehyde (500 mg/L, 800 mg/L, 100 mg/L, 1 500 mg/L, and 2 000 mg/L) at 37°C, 200 r/min. The OD600 was detected after 48 h to determine whether these bacteria could tolerate the acetaldehyde.
To further investigate the abilities of acetaldehyde-degradation of these bacteria, acetaldehyde was used as sole carbon for the growth of these bacteria (1 g/L NH4NO3, 500 mg/L acetaldehyde and sea water). Acetaldehyde-degrading bacteria cells were cultured at 37°C, 200 r/min for 24 h in 2216E medium. The cultures were centrifuged at 10 000 g for 10 min, and the bacterial cells were collected. The cells pellets were washed twice with sterile medium (1 g/L NH4NO3 and sea water), and then resuspended in medium (1 g/L NH4NO3 and sea water). Subsequently, acetaldehyde-degrading bacteria (2% inoculation amount) were cultured in medium (1 g/L NH4NO3, 500 mg/L acetaldehyde and sea water) at 37°C, 200 r/min for 24 h and the medium without acetaldehyde-degrading bacteria were used as the blank control. Then, the cultures were centrifuged at 10 000 g for 10 min, and the supernatants were collected to analysis acetaldehyde using HPLC. Previous reporters have described the method of detecting acetaldehyde, 200 μL 1 000 mg/L of 2, 4-dinitrophenylhydrazine (DNPH) and 20 μL acetic acid was added to each of 200 μL samples supernatants and incubated for 15 min at 37°C for derivatization. Each of samples were mixed with 1 200 μL extraction agent (ethyl acetate:n-hexane=1:5, v/v) for vortex shocked 5 min, and then sat for 30 min, supernatants were collected and then were vacuum-dried for 6 h using a speed vacuum concentrator (Labconco, Kansas City, MO, USA). The derivative samples were re-dissolved in solution (acetonitrile:water=85:15, v/v) and then analyzed by Agilent E2695 (Agilent Technologies, Wilmington, DE, USA) equipped with Acclaim 120 C18 (4.6 mm×250 mm) and 2998 PDA detector. Samples were analyzed at 40°C using ethyl acetate:n-hexane=1:5 (v/v) as a mobile phase at a flow rate of 1 mL/min. The concentration of the acetaldehyde-DNPH (ACH-DNPH) was determined by the calibration curves of peak areas vs. the standard curve of acetaldehyde-DNPH, which were obtained from HPLC analysis. In addition, the concentration of acetaldehyde in the blank control was detected to calculate the volatilization of acetaldehyde during cultivation.
2.6 Nucleotide sequence accession number
Bacterial 16S rRNA sequences obtained in this study were deposited in GenBank under accession numbers KM873053-KM873119 and KM873133–KM873144.
3 Results
Less
3.1 Uncultivated acetaldehyde-degrading bacterial community composition of the West Pacific Ocean’s deep sea in laboratory and in situ
To analyze acetaldehyde-degrading bacterial community in deep sea water of the West Pacific Ocean, two sample treatments including enrichment in laboratory and in situ were used. To further measure the bacterial diversity presented within two different samples, a series of alpha diversity indices were used (Table 1). Coverages were 91.5% and 92.5% for enrichment in laboratory and in situ, respectively, which showed these data were authentic. Shannon, Simpson, and Chao1 diversity indices account for evenness and richness as well as the total number of species obtained. The overall diversity of bacterial populations was showed with Shannon diversity index of 2.29 and 2.07, Evenness index of 0.654 9 and 0.597 2, Chao1 richness estimator of 101 and 40.75 in sample of enrichment in laboratory and in situ, receptively.
As showed in Table 2, a total of 33 and 32 OTUs were obtained from 200 clones in sample of enrichment in laboratory and in situ, respectively. To identify these OTUs, BLASTn database was used for 16S rRNA gene identification, and then MEGA 5.0 was employed for phylogenetic analysis. In laboratory, three OTUs belonging to Vibrio genus were obtained: OTU ACH-14L-309 and ACH-14L-70 exhibited 99% and 97% 16S rRNA gene similarities to Vibrio harveyi ATCC BAA-1116, respectively. OTU ACH-14L-307 showed 98% 16S rRNA gene similarity to Vibrio crassostreae strain LGP 7, OTU ACH-14L-308 exhibited 99% 16S rRNA gene similarity to Streptococcus pseudopneumoniae IS7493, and OTU ACH-14L-306 showed 99% 16S rRNA gene similarity to Halomonas meridiana strain DSM 5425, OTU ACH-14L-67 showed 94% 16S rRNA gene similarity to Thalassobacter stenotrophicus strain 5SM22, OTU ACH-14L-86 exhibited 99% 16S rRNA gene similarity with Staphylococcus caprae strain ATCC 35538, OTU ACH-14L-287 showed 99% 16S rRNA gene similarity with Marinobacter vinifirmus strain FB1, and two OTUs which belonged to Desulfuromusa genus were obtained, namely OTU ACH-14L-77 and ACH-14L-60 which have showed 97% and 96% 16S rRNA gene similarities to Desulfuromusa ferrireducens strain 102 and Desulforhopalus singaporensis strain S’pore T1, respectively. In situ, two OTUs belonging to Vibrio genus were also obtained, namely OUT ACH-14S-98 and OTU ACH-14S-76 which have 99% 16S rRNA gene similarities to Vibrio harveyi ATCC BAA-1116 and Vibrio chagasii strain R-3712, respectively. OTU ACH-14S-95 showed 99% 16S rRNA gene similarity with Halomonas meridiana strain DSM 5425. OTU ACH-14S-85 exhibited 95% 16S rRNA gene similarity with Pelagicola litoralis strain CL-ES2. Four OTUs belonging to marinobacter genus were obtained: OTU ACH-14S-211, ACH-14S-74, ACH-14S-63 and ACH-14S-68. All of OTUs’ information in laboratory or in situ was shown in Table 2.
3.2 Comparing of uncultivated acetaldehyde-degrading bacterial diversity of the West Pacific Ocean’s deep sea in laboratory and in situ
Previous studies have showed that different ways of sample treatments could enrich different bacteria (Rochelle et al., 1994; Smalla et al., 2007). Eight bacterial phyla were detected, while two OTUs were unclassified. As showed in Fig. 1, the most predominant phyla was γ-proteobacteria (63.5%), followed by Firmicutes (14%), α-proteobacteria (6.5%), β-proteobacteria (5%), δ-proteobacteria (4%), Cyanobacteria (3%), ε-proteobacteria (2.5%), Actinobacteria (1%) and 0.5% unclassified in sample of enrichment in laboratory. And γ-proteobacteria (75%) was also the most predominant phyla in sample of enrichment in situ, followed by Firmicutes (11%), α-proteobacteria (6%), δ-proteobacteria (2.5%), Actinobacteria (2.5%), ε-proteobacteria (2%), Cyanobacteria (0.5%) and 0.5% unclassified in sample of enrichment in situ, while β-proteobacteria was not obtained (Fig. 2). These results showed that bacteria of γ-proteobacteria were the main bacterial population whether sample enrichment performed in laboratory or in situ, and also predicted that these bacteria may play key roles in the degradation of acetaldehyde in sea. These results also indicated there was no significant difference between uncultivated acetaldehyde-degrading bacteria from sample of enrichment in situ and in laboratory in phyla level.
In genus level, uncultivated acetaldehyde-degrading bacteria community structure was different between enrichments in laboratory and in situ (Fig. 3). In situ, a total of 24 genus were detected from 200 clones, and vibrio was the most abundant genus accounting for 48.5% of all clones, followed by halomonas (9%), pseudoalteromonas (7%), bacillus (6%), pelagicola (5.5%), marinobacter (4.5%), dolosigranulum (3.5%), desulforhopalus (2.5%), escherichia, alteromonas and propionibacterium accounting for 1.5%, and the other genus were less than 1%. While in laboratory, a total of 27 genus were detected, and vibrio was also the most abundant genus accounting for 45% of all clones, followed by streptococcus (6%), halomonas (5.5%), neisseria, thalassobacter and staphylococcus (5%), marinobacter (4.5%), desulforhopalus (3.5%), trichodesmium (3%), idiomarina (2.5%), alteromonas (2%), escherichia, sulfurovum and bacillus accounting for 1.5%, and the other genus were less than 1%. Although uncultivated acetaldehyde-degrading bacteria community structure was different, vibrio was the most predominant genus whether enrichments were performed in laboratory or in situ, which was in accord with previous studies. These results maybe deduced that bacteria which belonged to vibrio genus were the main bacterial population for acetaldehyde-degrading bacteria community in deep sea.
3.3 Isolation of acetaldehyde-degrading bacteria of the west Pacific Ocean’s deep sea in laboratory and in situ
To further screen and investigate the acetaldehyde-degrading bacteria of the West Pacific Ocean’s deep sea, we have isolated cultivable bacteria from deep sea water which were enriched in laboratory and in situ. In laboratory, a total of four acetaldehyde-degrading strains were obtained (Table 3). Two strains belonging to vibrio genus were obtained, namely, strain ACH-L-1 and strain ACH-L-2 which exhibited 99% 16S rRNA gene similarities with vibrio harveyi ATCC BAA-1116 and vibrio rotiferianus CAIM 577, respectively. One strain ACH-L-5 showed 99% 16S rRNA gene similarity with halomonas axialensis strain Althf1 and another strain ACH-L-8 exhibited 99% 16S rRNA gene similarity with halomonas meridiana strain DSM 5425. While in situ, a total of eight acetaldehyde-degrading strains were isolated. Strain ACH-S-1 showed 99% 16S rRNA gene similarity to vibrio rotiferianus CAIM 577 and it was also obtained in laboratory. Another strain, namely, ACH-S-12 has shown 99% 16S rRNA gene similarity to vibrio parahaemolyticus RIMD 2210633. Strain ACH-S-6 which belonged to halomonas genus exhibited 16S rRNA gene similarity to halomonas axialensis strain Althf1. Furthermore, two strains as well as ACH-S-7 and ACH-S-10 have showed 97% and 99% 16S rRNA gene similarity to pseudoalteromonas piscicida strain IAM 12932 and pseudomonas xanthomarina strain KMM 1447, respectively. Strains ACH-S-8 and ACH-S-9 which showed 99% 16S rRNA gene similarity to bacillus aquimaris strain TF-12 were obtained. Another strain ACH-S-11 exhibited 99% 16S rRNA gene similarity to pseudomonas xanthomarina strain KMM 1447. These results showed that bacteria belonging to vibrio and halomonas were the main bacterial population for acetaldehyde-degrading bacterial community in deep sea. Furthermore, these results also showed that bacteria of vibrio and halomonas genus are more suitable for cultivation in laboratory’s conditions than other bacteria.
3.4 Ability of acetaldehyde-degrading for cultivable acetaldehyde-degrading bacteria
To further investigate the ability of acetaldehyde-degrading of these strains, we have detected the tolerance of cultivable acetaldehyde-degrading bacteria suffering acetaldehyde and the degradation of acetaldehyde by using HPLC analysis. In Table 3, our results have showed that all of strains can grow in medium which contain high concentration of acetaldehyde (0.8–1.5 mg/mL). There were three strains, namely, ACH-L-5, ACH-L-8 and ACH-S-12 can tolerate 1.5 g/L acetaldehyde. Follow eight strains, ACH-L-2, ACH-S-1, ACH-S-6, ACH-S-7, ACH-S-10, ACH-S-11, ACH-S-8 and ACH-S-9 can suffer 1 g/L acetaldehyde. Strain ACH-L-1 can tolerate 0.8 g/L acetaldehyde. Then we have detected the ability of acetaldehyde-degrading of these strains by using acetaldehyde as sole carbon for growth. We have found that most of strains can degrade acetaldehyde. In particular, there were four strains, namely ACH-L-5, ACH-L-8, ACH-S-12 and ACH-S-6, could degrade all of acetaldehyde in medium (500 mg/L) after 24 h. Followed by strain ACH-S-11 which could degrade 82.94% acetaldehyde, strain ACH-S-9 was 73.92%, strain ACH-S-8 have degraded 55.44%, and strains ACH-L-2, ACH-L-1, ACH-S-7, ACH-S-1, ACH-S-10 have degraded 53.90%, 50.40%, 39.50%, 27.00% and 17.10% acetaldehyde, respectively. As shown in Table 4, these results showed that bacteria belonging to the genus Halomonas have better ability of acetaldehyde degradation than other genus’ bacteria.
4 Discussion
Less
Although, a large number of marine microorganism species have been reported, the vast majority was still unknown (Ding and Valentine, 2015; Arrigo, 2005). Meanwhile, marine microorganisms were more and more used in many fields, including biomedicine, industrial production, environmental management, and the study of marine microorganisms always was one of the hot spots over the last decades (Gao et al., 2017; Bernan et al., 1997; Kelecom, 2002). Deep sea water could also harbor many microorganisms, especially some typical microorganisms with bioactive functions, such as acetaldehyde-degrading bacteria and polysaccharides-degrading bacteria (Horikoshi, 1998; Koyama and Yoshida, 2016). In previous studies, bacterial diversity studies were analyzed by using streak plate method, sequencing of 16S rRNA (Caporaso et al., 2011). While most of these studies were performed in laboratory. To further investigate the diversity of acetaldehyde-degrading bacteria in the West Pacific Ocean’s deep sea. We have analyzed the diversity of cultured and uncultured acetaldehyde-degrading bacteria of deep sea water which were enriched in laboratory and in situ by using streak plate method and sequencing of 16S rRNA. Meanwhile, we also have detected the ability of acetaldehyde-degradation of these cultured bacteria. Our studies have showed that α, γ, δ, ε-Proteobacteria, Actinobacteria, Firmicutes, Cyanobacteria dominated the bacterial community by sequencing of 16S rRNA in deep sea water with enrichments in laboratory or in situ. But there were only some strains which belonged to γ-Proteobacteria and Firmicutes were obtained by using streak plate method. Meanwhile, these results indicated that most of acetaldehyde-degrading bacteria in deep sea water were not suitable for growth in laboratory’s conditions. On the other hand, as shown in Table 1, the uncultured bacterial diversity richness which enrichment in laboratory is better than enrichment in situ. Although the bacterial diversity richness in laboratory is better than in situ, but the main bacterial community structures are similar. Thus, our study has showed that bacteria of Vibrio and Halomonas composed the dominant population. Conversely, we have obtained more acetaldehyde-degrading bacterial strains in situ than in laboratory. It seems that more uncultured bacteria were enriched in laboratory conditions than in situ conditions, while bacterial strains were suitable grown in situ environments. We have also demonstrated that these bacteria belonging to genus Vibrio and Halomona played a key role in degradation of aldehydes material of marine.
In phylum level, previous studies have demonstrated that bacteria of Proteobacteria dominated bacterial community in environments, contain α, γ, δ, and ε-Proteobacteria (O’Sullivan et al., 2002; Franzmann, 1996; Borneman and Triplett, 1997). Previous studies of marine bacterial diversity have showed that bacteria belonging to α-Proteobacteria were the main uncultured bacterial species, while the main cultured bacterial species were the γ-Proteobacteria (Borneman and Triplett, 1997). Interestingly, in this study, γ-Proteobacteria were the dominating bacteria whether cultured or uncultured bacteria. In genus level, Vibrio and Halomonas were the dominating genus of uncultured bacteria, and we have obtained some strains belonging to Vibrio and Halomonas, especially only strains of Vibrio and Halomona were found from enrichment in laboratory. The results of detecting ability of acetaldehyde-degrading have showed these strains belonging to Vibrio and Halomona were better than the other strains for the ability of acetaldehyde-degrading. It seems that bacteria of Vibrio and Halomona play a key role in the degradation of acetaldehyde in deep sea water. Similarly, previous studies have reported that bacteria of Vibrio and Halomona could grow in the high aldehydes concentration (Vedadi and Meighen, 1997; Sripo et al., 2002), but further and systemic investigation should be carried out. In our study, we investigated the diversity of bacteria of acetaldehyde-degrading in deep sea water of the West Pacific Ocean, and compared the different diversity of acetaldehyde-degrading bacteria between with two samples which enrichment in situ and in laboratory. Some acetaldehyde-degrading bacterial strains were obtained, especially four strains belonging to Vibrio and three strains of Halomonas, which have potentials in degradation of aldehydes material.
Previous studies have reported a strain, namely Acetobacter pasteurianus belonging to Rhodobacterales, α-Proteobacteria, which have utilized acetaldehyde or ethanol in medium as carbon source for growth (Kanchanarach et al., 2010; Takemura et al., 1993). In this study, 16S rRNA genes of Rhodobacterales and Rhizobiales were also found, it indicates that these bacteria belonging to α-Proteobacteria play key roles in carbon or nitrogen cycles in marine environments. Unfortunately, bacterial strains of α-Proteobacteria were not isolated because of unsuitable culture condition. Previous reports have investigated typical marine bacterial diversity and found that these bacteria belonging to β-Proteobacteria mainly survive in estuary or nearshore area and almost not distribute in deep sea (Sekiguchi et al., 2002; Wu et al., 2004). Similarly, our studies do not find bacteria belonging to β-Proteobacteria, except one 16S rRNA gene from enrichment in situ. The bacteria of δ, ε-Proteobacteria which have ability of sulfate reducing or sulfur-oxidizing were frequently found in hydrothermal area and cold seep of deep sea. Meanwhile, in this study, we also have obtained 16S rRNA genes of δ, ε-Proteobacteria from the deep sea water whether enrichment in situ or in laboratory. These results may suggest that these bacteria may play important roles in marine carbon cycling and nitrogen cycling.
Bacteria of Firmicutes were frequently isolated from offshore and sediment in shallow sea, and there were debatable about it was marine aborigines or originate from mainland (Ravenschlag et al., 1999). Meanwhile, the bacteria belonging to Enterococcus, Planomicrobium, Bacillus, have showed that the ability of degrading acetaldehyde. In this study, not only 16S rRNA genes of Firmicutes were detected, but also cultured bacteria of Enterococcus, Planomicrobium, Bacillus (belong to Firmicutes) were isolated. As far as we know, this was the first reportthat the cultured bacteria of Firmicutes from deep sea could degrade acetaldehyde.
As we all know that there are a larger number of microorganism species in ocean, and many of marine microorganisms have excellent bioactivities for application (Kobayashi and Ishibashi, 1993; Okami et al., 1976; Manivasagan et al., 2016). Unfortunately, most of marine microorganisms are still unknown. In our study, we have screened 16S rRNA genes of uncultured bacteria and isolated cultured bacteria from the deep sea water of the West Pacific Ocean by using enrichment in situ and in the laboratory, and then detected the ability of acetaldehyde-degradation of cultured bacteria, respectively. Our study showed that the γ-Proteobacteria (occupied 80% clones) was dominant in the deep sea water of the West Pacific Ocean, especially these bacteria belonging to Vibrio and Halomonas were widely distributed in deep sea environments and composed the main acetaldehyde-degrading bacterial community in deep sea water whether enrichment in situ or laboratory. As far as we known, this is the first systematic report of acetaldehyde-degrading bacteria in the deep sea water of the West Pacific Ocean. Our study will provide a reference for investigation of acetaldehyde-degrading bacteria in the West Pacific Ocean. Based on above investigations, the potential applications of acetaldehyde-degrading bacterial stains from the deep sea water of the West Pacific Ocean was suggested.
Funding
Less
  • The Xiamen Ocean Economic Innovation and Development Demonstration Project under contract No. 16PZP001SF16.
References
Less
Arrigo K R. 2005. Marine microorganisms and global nutrient cycles. Nature, 437(7057): 349–355
Bernan V S, Greenstein M, Maiese W M. 1997. Marine microorganisms as a source of new natural products. Advances in Applied Microbiology, 43: 57–90
Borneman J, Triplett E W. 1997. Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation. Applied and Environmental Microbiology, 63(7): 2647–2653
Caporaso J G, Lauber C L, Walters W A, et al. 2011. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the National Academy of Sciences of the United States of America, 108(S1): 4516–4522
Chao Anne. 1984. Nonparametric estimation of the number of classes in a population. Scandinavian Journal of Statistics, 11(4): 265–270
Chao Anne, Lee S M. 1992. Estimating the number of classes via sample coverage. Journal of the American Statistical Association, 87(417): 210–217
Chao Anne, Shen T J. 2003. Nonparametric estimation of Shannon’s index of diversity when there are unseen species in sample. Environmental and Ecological Statistics, 10(4): 429–443
Ding Haibing, Valentine D L. 2008. Methanotrophic bacteria occupy benthic microbial mats in shallow marine hydrocarbon seeps, Coal Oil Point, California. Journal of Geophysical Research: Biogeosciences, 113(G1): G01015
Ding H, Valentine D L. 2015. Methanotrophic bacteria occupy benthic microbial mats in shallow marine hydrocarbon seeps, Coal Oil Point, California. Journal of Geophysical Research Biogeosciences, 113(G1): 222–256
Franzmann P D. 1996. Examination of Antarctic prokaryotic diversity through molecular comparisons. Biodiversity and Conservation, 5(11): 1295–1305
Gao Boliang, Jin Min, Li Li, et al. 2017. Genome sequencing reveals the complex polysaccharide-degrading ability of novel deep-sea bacterium Flammeovirga pacifica WPAGA1. Front Microbiol, 8: 600
Gesser H D, Fu Shali. 1990. Removal of aldehydes and acidic pollutants from indoor air. Environmental Science & Technology, 24(4): 495–497
Homann N, Tillonen J, Meurman J H, et al. 2000. Increased salivary acetaldehyde levels in heavy drinkers and smokers: a microbiological approach to oral cavity cancer. Carcinogenesis, 21(4): 663–668
Horikoshi K. 1998. Barophiles: deep-sea microorganisms adapted to an extreme environment. Current Opinion in Microbiology, 1(3): 291–295
Ista L K, Callow M E, Finlay J A, et al. 2004. Effect of substratum surface chemistry and surface energy on attachment of marine bacteria and algal spores. Applied and Environmental Microbiology, 70(7): 4151–4157
Kaeberlein T, Lewis K, Epstein S S. 2002. Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment. Science, 296(5570): 1127–1129
Kanchanarach W, Theeragool G, Yakushi T, et al. 2010. Characterization of thermotolerant Acetobacter pasteurianus strains and their quinoprotein alcohol dehydrogenases. Applied Microbiology and Biotechnology, 85(3): 741–751
Kelecom A. 2002. Secondary metabolites from marine microorganisms. Anais da Academia Brasileira de Ciências, 74(1): 151–170
Kirk J L, Beaudette L A, Hart M, et al. 2004. Methods of studying soil microbial diversity. Journal of Microbiological Methods, 58(2): 169–188
Kobayashi J, Ishibashi M. 1993. Bioactive metabolites of symbiotic marine microorganisms. Chemical Reviews, 93(5): 1753–1769
Koyama S, Yoshida T. 2016. Electrical collection of membrane-intact and dehydrogenase-positive symbiotic bacteria from the deep-sea bivalve Calyptogena Okutanii. Electrochemistry, 84(5): 358–360
Kurkivuori J, Salaspuro V, Kaihovaara P, et al. 2007. Acetaldehyde production from ethanol by oral streptococci. Oral Oncology, 43(2): 181–186
Lachenmeier D W, Sohnius E M. 2008. The role of acetaldehyde outside ethanol metabolism in the carcinogenicity of alcoholic beverages: evidence from a large chemical survey. Food and Chemical Toxicology, 46(8): 2903–2911
Li Erhu, de Orduña R M. 2011. Evaluation of the acetaldehyde production and degradation potential of 26 enological Saccharomyces and non-Saccharomyces yeast strains in a resting cell model system. Journal of Industrial Microbiology & Biotechnology, 38(9): 1391–1398
Lubin M, Westerfield W W. 1945. The metabolism of acetaldehyde. Journal of Biological Chemistry, 161: 503–512
Manivasagan P, Nam S Y, Oh J. 2016. Marine microorganisms as potential biofactories for synthesis of metallic nanoparticles. Critical Reviews in Microbiology, 42(6): 1007–1019
Okami Y, Okazaki T, Kitahara T, et al. 1976. Studies on marine microorganisms. V. A new antibiotic, aplasmomycin, produced by a Streptomycete isolated from shallow sea mud. Journal of Antibiotics, 29(10): 1019–1025
Okazaki T, Kitahara T, Okami Y. 1975. Studies on marine microorganisms: IV. A new antibiotic SS-228 Y produced by Chainia isolated from shallow sea mud. Journal of Antibiotics, 28(3): 176–184
O’Sullivan L A, Weightman A J, Fry J C. 2002. New degenerate Cytophaga-Flexibacter-Bacteroides-Specific 16S ribosomal DNA-targeted oligonucleotide probes reveal high bacterial diversity in river taff epilithon. Applied and Environmental Microbiology, 68(1): 201–210
Ravenschlag K, Sahm K, Pernthaler J, et al. 1999. High bacterial diversity in permanently cold marine sediments. Applied and Environmental Microbiology, 65(9): 3982–3989
Rochelle P A, Cragg B A, Fry J C, et al. 1994. Effect of sample handling on estimation of bacterial diversity in marine sediments by 16S rRNA gene sequence analysis. FEMS Microbiology Ecology, 15(1–2): 215–225
Sekiguchi H, Koshikawa H, Hiroki M, et al. 2002. Bacterial distribution and phylogenetic diversity in the Changjiang estuary before the construction of the Three Gorges Dam. Microbial Ecology, 43(1): 82–91
Smalla K, Oros-Sichler M, Milling A, et al. 2007. Bacterial diversity of soils assessed by DGGE, T-RFLP and SSCP fingerprints of PCR-amplified 16S rRNA gene fragments: do the different methods provide similar results?. Journal of Microbiological Methods, 69(3): 470–479
Sripo T, Phongdara A, Wanapu C, et al. 2002. Screening and characterization of aldehyde dehydrogenase gene from Halomonas salina strain AS11. Journal of Biotechnology, 95(2): 171–179
Svegliati-Baroni G, Ridolfi F, Di Sario A, et al. 2001. Intracellular signaling pathways involved in acetaldehyde-induced collagen and fibronectin gene expression in human hepatic stellate cells. Hepatology, 33(5): 1130–1140
Takemura H, Kondo K, Horinouchi S, et al. 1993. Induction by ethanol of alcohol dehydrogenase activity in Acetobacter pasteurianus. Journal of Bacteriology, 175(21): 6857–6866
van der Ploeg J, Smidt M P, Landa A S, et al. 1994. Identification of chloroacetaldehyde dehydrogenase involved in 1,2-dichloroethane degradation. Applied and Environmental Microbiology, 60(5): 1599–1605
Vedadi M, Meighen E. 1997. Critical glutamic acid residues affecting the mechanism and nucleotide specificity of Vibrio harveyi aldehyde dehydrogenase. European Journal of Biochemistry, 246(3): 698–704
Wu M, Song Liansheng, Ren Jianping, et al. 2004. Assessment of microbial dynamics in the Pearl River Estuary by 16S rRNA terminal restriction fragment analysis. Continental Shelf Research, 24(16): 1925–1934
Xi Zhuge, Dai Shugui, Zhang Lin, et al. 1999. Studies on the damage of calf thymus DNA induced by 3 kinds of aldehyde pollutants using ultraviolet and fluorescence spectrum. Environmental Chemistry (in Chinese), 18(5): 453–457
Zhou Zhijun, Liu Yingxi, Zeng Junning, et al. 2005. Determination of 13 kinds of aldehyde and ketone pollutants of indoor air by HPLC at one time. Journal of Environment and Health (in Chinese), 22(4): 297–299
Appendix
Less
Year 2018 volume 37 Issue 8
PDF
32
17
Cite this Article
BibTeX
Article Info
doi: 10.1007/s13131-018-1235-z
  • Receive Date：2017-12-14
  • Online Date：2026-04-14
  • Published：2018-08-25
Article Data
Affiliations
History
  • Received：2017-12-14
  • Accepted：2018-03-13
Funding
The Xiamen Ocean Economic Innovation and Development Demonstration Project under contract No. 16PZP001SF16.
Affiliations
    1 School of Life Sciences, Xiamen University, Xiamen 361102, China
    2 State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, China
    3 Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen 361005, China

Corresponding:

References
Share
https://castjournals.cast.org.cn/joweb/aos/EN/10.1007/s13131-018-1235-z
Share to
QR

Scan QR to access full text

Cite this article
BibTeX
Citations
表12种不同金属材料的力学参数
科
Family		 属数
Number of
genus		 种数
Number of
species		 占总种数比例
Percentage of
total species (%)		 属
Genus		 种数
Number of
species		 占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
关闭全屏
  • BibTeX
  • EndNote
  • RefWorks
  • TxT
Links
Articles
Latest Articles
Most Read
Collections
Updates
Events
News
Multimedia
About
About Us
Contact
No. 86 Xueyuan South Road, Haidian District, Beijing
100081
010-62199257
qkjq@cast.org.cn

Copyright © 2025 China Association for Science and Technology. All rights reserved. For all open access content, the relevant licensing terms apply.
Sponsored by the Office of the Leading Group for Cybersecurity and Informatization of CAST, and supported by Science and Technology Review Publishing House