Evaluation of carbon storage in soil and plant biomass of primary and secondary mixed deciduous forests in the lower northern part of Thailand

Carbon sequestration in a forest ecosystem is an important determinant of the local and regional carbon stock. This study monitored forest types and carbon storage in both biomass and soil within primary mixed deciduous forests (PMDF) and secondary mixed deciduous forests (SMDF). One study plot measuring 50 x 50 m and five 10 x 10 m plots were set up at each study site for trees and shrubs inventory, respectively. The trees and shrubs were counted and identified by species. Organic carbon in biomass was estimated by using allometry equation and soil carbon concentration was analyzed by Walkley-Black method. The results revealed that PMDF had a higher level of carbon storage in biomass than SMDF by approximately two times, while soil carbon stock in PMDF was also quite higher than SMDF. The dominant species having a high carbon concentration included Canarium subulatum, Pterocarpus macrocarpus, Dalbergia cultrate, Lagerstroemia tomentosa and Xylia xylocarpa var kerrii. These species were found in intermediate succession, thus indicating that some may be suitable for replanting in future restoration processes in order to accelerate natural succession and storage carbon. This may be one method to reduce the CO2 in the atmosphere by making the SMDF act as a carbon sink.Key words: Thailand, carbon storage, soil, plant biomass, mixed deciduous forest, northern

Description of Streptomyces naphthomycinicus sp. nov., an endophytic actinobacterium producing naphthomycin A and its genome insight for discovering bioactive compounds

Endophytic actinobacteria are a group of bacteria living inside plant tissue without harmful effects, and benefit the host plant. Many can inhibit plant pathogens and promote plant growth. This study aimed to identify a strain of Streptomyces as a novel species and study its antibiotics production. An endophytic actinobacterium, strain TML10T was isolated from a surface-sterilized leaf of a Thai medicinal plant (Terminalia mucronata Craib and Hutch). As a result of a polyphasic taxonomy study, strain TML10T was identified as a member of the genus Streptomyces. Strain TML10T was an aerobic actinobacterium with well-developed substrate mycelia with loop spore chains and spiny surface. Chemotaxonomic data, including cell wall components, major menaquinones, and major fatty acids, confirmed the affiliation of strain TML10T to the genus Streptomyces. The results of the phylogenetic analysis, including physiological and biochemical studies in combination with a genome comparison study, allowed the genotypic and phenotypic differentiation of strain TML10T and the closest related type strains. The digital DNA-DNA hybridization (dDDH), Average nucleotide identity Blast (ANIb), and ANIMummer (ANIm) values between strain TML10T and the closest type strain, Streptomyces musisoli CH5-8T were 38.8%, 88.5%, and 90.8%, respectively. The name proposed for the new species is Streptomyces naphthomycinicus sp. nov. (TML10T = TBRC 15050T = NRRL B-65638T). Strain TML10T was further studied for liquid and solid-state fermentation of antibiotic production. Solid-state fermentation with cooked rice provided the best conditions for antibiotic production against methicillin-resistant Staphylococcus aureus. The elucidation of the chemical structures from this strain revealed a known antimicrobial agent, naphthomycin A. Mining the genome data of strain TML10T suggested its potential as a producer of antbiotics and other valuable compounds such as ε-Poly-L-lysine (ε-PL) and arginine deiminase. Strain TML10T contains the arcA gene encoding arginine deiminase and could degrade arginine in vitro

Meta-barcoded evaluation of the ISO standard 11063 DNA extraction procedure to characterize soil bacterial and fungal community diversity and composition

This study was designed to assess the influence of three soil DNA extraction procedures, namely the International Organization for Standardization (ISO-11063, GnS-GII and modified ISO procedure (ISOm), on the taxonomic diversity and composition of soil bacterial and fungal communities. The efficacy of each soil DNA extraction method was assessed on five soils, differing in their physico-chemical characteristics and land use. A meta-barcoded pyrosequencing approach targeting 16S and 18S rRNA genes was applied to characterize soil microbial communities. We first observed that the GnS-GII introduced some heterogeneity in bacterial composition between replicates. Then, although no major difference was observed between extraction procedures for soil bacterial diversity, we saw that the number of fungal genera could be underestimated by the ISO-11063. In particular, this procedure underestimated the detection in several soils of the genera Cryptococcus, Pseudallescheria, Hypocrea and Plectosphaerella, which are of ecological interest. Based on these results, we recommend using the ISOm method for studies focusing on both the bacterial and fungal communities. Indeed, the ISOm procedure provides a better evaluation of bacterial and fungal communities and is limited to the modification of the mechanical lysis step of the existing ISO-11063 standard

Pseudonocardia hispaniensis sp. nov., a novel actinomycete isolated from industrial wastewater activated sludge

A novel actinomycete, designated PA3T, was isolated from an oil refinery wastewater treatment plant, located in Palos de la frontera, Huelva, Spain, and characterized taxonomically by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate formed a distinct subclade in the Pseudonocardia tree together with Pseudonocardia asaccharolytica DSM 44247T. The chemotaxonomic properties of the isolate, for example, the presence of MK-8 (H4) as the predominant menaquinone and iso-C16:0 as the major fatty acid are consistent with its classification in the genus Pseudonocardia. DNA:DNA pairing experiments between the isolate and the type strain of P. asaccharolytica DSM 44247T showed that they belonged to separate genomic species. The two strains were readily distinguished using a combination of phenotypic properties. Consequently, it is proposed that isolate PA3T represents a novel species for which the name Pseudonocardia hispaniensis sp. nov. is proposed. The type strain is PA3T (= CCM 8391T = CECT 8030T).Cuesta Amat, G.; Soler Hernández, A.; Alonso Molina, JL.; Ruvira, M.; Lucena, T.; Arahal, D.; Goodfellow, M. (2013). Pseudonocardia hispaniensis sp. nov., a novel actinomycete isolated from industrial wastewater activated sludge. Antonie van Leeuwenhoek. 103(1):135-142. doi:10.1007/s10482-012-9792-1S1351421031Alonso JL, Cuesta G, Ramírez GW, Morenilla JJ, Bernácer I, Lloret RM (2009) Manual de técnicas avanzadas para la identificación y control de bacterias filamentosas. Epsar-Generalitat Valenciana, España, p 21–36Ara I, Tsetseg B, Daram D, Suto M, Ando K (2011) Pseudonocardia mongoliensis sp. nov. and Pseudonocardia khuvsgulensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 61:747–756Arahal DR, Sánchez E, Macián MC, Garay E (2008) Value of recN sequences for species identification and as a phylogenetic marker within the family ‘‘Leuconostocaceae’’. Int Microbiol 11:33–39Auffret M, Labbé D, Thouand G, Greer CW, Fayolle-Guichard F (2009) Degradation of a mixture of hydrocarbons, gasoline, and diesel oil additives by Rhodococcus aetherivorans and Rhodococcus wratislaviensis. Appl Environ Microbiol 75:7774–7782Cashion P, Hodler-Franklin MA, McCully J, Franklin M (1977) A rapid method for base ratio determination of bacterial DNA. Anal Biochem 81:461–466Chen HH, Qin S, Li J, Zhang YQ, Xu LH, Jiang CL, Kim CJ, Li WJ (2009) Pseudonocardia endophytica sp. nov., isolated from pharmaceutical plant Lobelia clavata. Int J Syst Evol Microbiol 59:559–563De Ley J, Cattoir H, Reynaerts A (1970) The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142Duangmal K, Thamchaipenet A, Matsumoto A, Takahashi Y (2009) Pseudonocardia acaciae sp. nov., isolated from roots of Acacia auriculiformis A. Cunn. ex Benth. Int J Syst Evol Microbiol 59:1487–1491Gordon RE, Barnett DA, Handerhan JE, Pang CH-N (1974) Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 24:54–63Hamid ME, Minnikin DE, Goodfellow M, Ridell M (1993) Thin-layer chromatographic analysis of glycolipids and mycolic acids from Mycobacterium farcinogenes, Mycobacterium senegalense and related taxa. Zbl Bakt 279:354–367Hasegawa T, Takizawa M, Tanida S (1983) A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Microbiol 29:319–322Henssen A (1957) Beiträge zur Morphologie und Systematik der thermophilen Actinomyceten. Arch Mikrobiol 26:373–414Huang,Y, Goodfellow M (2012) Genus Pseudonocardia Hennsen 1957, 408VP emend. In: Goodfellow M, Kämpfer P, Busse H-J, Trujillo M, Suzuki KE, Ludwig W, Whitman WB (eds) Bergey’s manual of systematic bacteriology, 2nd edn, vol 5, part B. Springer, New YorkHuang Y, Wang L, Lu Z, Hong L, Liu Z, Tan GYA, Goodfellow M (2002) Proposal to combine the genera Actinobispora and Pseudonocardia in an emended genus Pseudonocardia, and description of Pseudonocardia zijingensis sp. nov. Int J Syst Evol Microbiol 52:977–982Huss VAR, Festl H, Schleifer KH (1983) Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4:184–192Kaewkla O, Franco CMM (2010) Pseudonocardia adelaidensis sp. nov., an endophytic actinobacterium isolated from the surface-sterilized stem of a grey box tree (Eucalyptus microcarpa). Int J Syst Evol Microbiol 60:2818–2822Kaewkla O, Franco CMM (2011) Pseudonocardia eucalypti sp. nov., an endophytic actinobacterium with a unique knobby spore surface, isolated from roots of a native Australian eucalyptus tree. Int J Syst Evol Microbiol 61:742–746Kämpfer P, Kohlweyer U, Thiemer B, Andreesen JR (2006) Pseudonocardia tetrahydrofuranoxydans sp. nov. Int J Syst Evol Microbiol 56:1535–1538Labeda DP, Goodfellow M, Chun J, Zhi XY, Li WJ (2011) Reassessment of the systematics of the suborder Pseudonocardineae: transfer of genera within the family Actinosynnemataceae Labeda and Kroppenstedt 2000 emend. Zhi et al. 2009 into an emended family Pseudonocardiaceae Embley et al. 1989 emend. Zhi et al. 2009. Int J Syst Evol Microbiol 61:1259–1264Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp 115–148Lechevalier MP, Lechevalier H (1970) Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 20:435–443Lechevalier MP, Stern AER, Lechevalier HA (1981) Phospholipids in the taxonomy of actinomycetes. Zbl Bakt Suppl 11:111–116Li J, Zhao GZ, Huang HY, Zhu WY, Lee JC, Kim CJ, Xu LH, Zhang LX, Li WJ (2010) Pseudonocardia rhizophila sp. nov., a novel actinomycete isolated from a rhizosphere soil. Antonie Van Leeuwenhoek 98:77–83Liu ZP, Wu JF, Liu ZH, Liu SJ (2006) Pseudonocardia ammonioxydans sp. nov., isolated from coastal sediment. Int J Syst Evol Microbiol 56:555–558Lucena T, Pascual J, Garay E, Arahal DR, Macián MC, Pujalte MJ (2010) Haliea mediterranea sp. nov., a new marine gammaproteobacterium. Int J Syst Evol Microbiol 60:1844–1848Ludwig W et al (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32:1363–1371Mahendra S, Alvarez-Cohen L (2005) Pseudonocardia dioxanivorans sp. nov., a novel actinomycete that grows on 1,4-dioxane. Int J Syst Evol Microbiol 55:593–598Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167MIDI (2008) Sherlock microbial identification system operating manual, version 6.1. MIDI Inc., NewarkMinnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241Nam S-W, Chun J, Kim S, Kim W, Zakrzewska-Czerwinska J, Goodfellow M (2003) Tsukamurella spumae sp. nov., a novel actinomycete associated with foaming in activated sludge plants. Syst Appl Microbiol 26:367–375Okoh A, Ajisebutu S, Babalola G, Trejo-Hernandez MR (2001) Potential of Burkholderia cepacia RQ1 in the biodegradation of heavy crude oil. Int Microbiol 4:83–87Park SW, Park ST, Lee JE, Kim YM (2008) Pseudonocardia carboxydivorans sp. nov., a carbon monoxide-oxidizing actinomycete, and an emended description of the genus Pseudonocardia. Int J Syst Evol Microbiol 58:2475–2478Pruesse E, Quast C, Knittel K, Fuchs B, Ludwig W, Peplies J, Glöckner FO (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35:7188–7196Qin S, Su YY, Zhang YQ, Wang HB, Jiang CL, Xu LH, Li WJ (2008) Pseudonocardia ailaonensis sp. nov., isolated from soil in China. Int J Syst Evol Microbiol 58:2086–2089Qin S, Zhu WY, Jiang JH, Klenk HP, Li J, Zhao GZ, Xu LH, Li WJ (2010) Pseudonocardia tropica sp. nov., an endophytic actinomycete isolated from the stem of Maytenus austroyunnanensis. Int J Syst Evol Microbiol 60:2524–2528Qin S, Xing K, Fei SM, Lin Q, Chen XM, Li WJ, Jiang JH (2011) Pseudonocardia sichuanensis sp. nov., a novel endophytic actinomycete isolated from the root of Jatropha curcus L. Antonie Van Leeuwenhoek 99:395–401Rehfuss M, Urban J (2005) Rhodococcus phenolicus sp. nov., a novel bioprocessor isolated actinomycete with the ability to degrade chlorobenzene, dichlorobenzene and phenol as sole carbon sources. Syst Appl Microbiol 28:695–701Reichert K, Lipski A, Pradella S, Stackebrandt E, Altendorf K (1998) Pseudonocardia asaccharolitica sp. nov. and Pseudonocardia sulfidoxidans sp. nov., two new dimethyl disulfide-degrading actinomycetes and emended description of the genus Pseudonocardia. Int J Syst Bacteriol 48:441–449Sakiyama Y, Thao NKN, Vinh HV, Giang NM, Miyadoh S, Hop DV, Ando K (2010) Pseudonocardia babensis sp. nov., isolated from plant litter. Int J Syst Evol Microbiol 60:2336–2340Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Tech Note 101:1–7Schäfer J, Busse HJ, Kämpfer P (2009) Pseudonocardia parietis sp. nov., from the indoor environment. Int J Syst Evol Microbiol 59:2449–2452Seviour RJ, Kragelund C, Kong Y, Eales K, Nielsen JL, Nielsen PH (2008) Ecophysiology of the actinobacteria in activated sludge systems. Antonie Van Leeuwenhoek 94:21–33Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340Staneck JL, Roberts GD (1974) Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28:226–231Warwick S, Bowen T, McVeigh HP, Embley TM (1994) A phylogenetic analysis of the family Pseudonocardiaceae and the genera Actinokineospora and Saccharothrix with 16S rRNA sequences and a proposal to combine the genera Amycolata and Pseudonocardia in an emended genus Pseudonocardia. Int J Syst Bacteriol 44:293–299Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Trüper HG (1987) International committee on systematic bacteriology report on the ad hoc committee on the reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464Yarza P, Ludwig W, Euzeby J, Amann R, Schleifer KH, Glöckner FO, Rossello-Mora R (2010) Update of the all-species living tree project based on 16S and 23S rRNA sequence analyses. Syst Appl Microbiol 33:291–299Zhao GZ, Li J, Zhu WY, Li XP, Tian SZ, Zhao LX, Xu LH, Li WJ (2011a) Pseudonocadia bannaensis sp. nov., a novel actinomycete isolated from the surface-sterilized roots of Artemisiae annua L. Antonie Van Leeuwenhoek 100:35–42Zhao GZ, Li J, Huang HY, Zhu WY, Zhao LX, Tang SK, Xu LH, Li WJ (2011b) Pseudonocardia artemisiae sp. nov., isolated from surface-sterilized Artemisia annua L. Int J Syst Evol Microbiol 61:1061–1065Zhao GZ, Li J, Huang HY, Zhu WY, Park DJ, Kim CJ, Xu LH, Li WJ (2011c) Pseudonocardia kunmingensis sp. nov., an actinobacterium isolated from surface-sterilized roots of Artemisia annua L. Int J Syst Evol Microbiol 61:2292–229

Nocardia callistridis sp. nov., an endophytic actinobacterium isolated from a surface-sterilized root of an Australian native pine tree

Reading, U

Tumbuhan etnoperubatan sebagai perumah aktinomiset endofit yang bersifat bioaktif(Ethnomedicinal plants as host of bioactive endophytic actinomycetes)

Sembilan Aktinomiset endofit telah berjaya dipencilkan daripada pokok yang mempunyai nilai ubatan dari beberapa tempat di Semenanjung Malaysia. Pencilan tersebut telah dikenalpasti melalui pemerhatian morfologi, amplifikasi gen 16S rRNA dan analisis penjujukan 16S rRNA. Saringan awal terhadap aktiviti antimikrob telah dilakukan dengan menggunakan teknik calitan plat. Pembentukan miselium substrat dan aerial, warna jisim spora, pigmen larut dan morfologi rantai spora pada semua pencilan menyerupai Streptomyces sp. dan Microbispora sp. Analisis filogenetik jujukan separa 16S rRNA mendapati pencilan SUK 08, SUK 10 dan SUK 15 saling berkaitan dengan Streptomyces eurythermus. Walau bagaimanapun pencilan ini telah dipencilkan dari tumbuhan yang berbeza. Pencilan ini didapati mempunyai aktiviti antimikrob terhadap bakteria dan kulat kajian. Empat pencilan aktif iaitu SUK 08, SUK 10, SUK 12 dan SUK 15 berupaya untuk membunuh dan merencat sehingga 100% satu atau lebih organisma patogen seperti Bacillus subtilis, Aspergillus fumigatus, Aspergillus niger, Fusarium solani, Rhizoctonia solani dan Trichoderma viride. Kajian ini mengesahkan bahawa tumbuhan etnoperubatan adalah sumber pencarian Aktinomiset endofit bioaktif yang berupaya menjadi sumber novel dalam pencarian agen antibakteria dan antimikotik