Functional metagenomics reveals differential chitin degradation and utilization features across free-living and host-associated marine microbiomes

Raimundo, I.; Silva, R.; Meunier, L.; Valente, S. M.; Lago-Lestón, A.; Keller-Costa, T.; Costa, R.

doi:10.1186/s40168-020-00970-2

Table 1 Chitin and chitin-derivative degradation capacities of marine sponge and octocoral-derived bacterial isolates

From: Functional metagenomics reveals differential chitin degradation and utilization features across free-living and host-associated marine microbiomes

Strain	Identity	Isolation source^a	Chitin degradation^b	Chitinase activity (units/mL)^c			*chiA* PCR^d	Genome sequence^e
Strain	Identity	Isolation source^a	Chitin degradation^b	EndoS3	ExoS1	ExoS2	*chiA* PCR^d	Genome sequence^e
Mc110	Micrococcus sp.	Sarcotragus spinosulus	−	−	−	−	−	No
EL33	Aquimarina sp.	Eunicella labiata	++	+	++	−	+	FLRG00000000.1
EL43	Aquimarina sp.	Eunicella labiata	++	+	++	−	+	No
Aq349	Aquimarina sp.	Sarcotragus spinosulus	++	+	+	−	+	OMKB00000000.1
Aq78	Aquimarina sp.	Sarcotragus spinosulus	++	+	+	−	+	OMKA00000000.1
Aq135	Aquimarina sp.	Ircinia variabilis	+	+	−	+	+	OMKE00000000.1
Aq107	Aquimarina sp.	Sarcotragus spinosulus	+	−	−	−	+	OMKC00000000.1
EL57	Aliivibrio sp.	Eunicella labiata	−	+	+	−	+	No
EL58	Aliivibrio sp.	Eunicella labiata	−	++	+	−	−	OMPC00000000.1
EL24	Enterovibrio sp.	Eunicella labiata	++	+	+	+	+	No
EL37	Enterovibrio sp.	Eunicella labiata	++	+	+	+	+	No
EL22	Vibrio sp.	Eunicella labiata	++	++	+	+	+	No
EL36	Vibrio sp.	Eunicella labiata	+	+	+	+	+	No
EL38	Vibrio sp.	Eunicella labiata	++	++	+	+	+	No
EL41	Vibrio sp.	Eunicella labiata	++	+	+	+	−	No
EL49	Vibrio sp.	Eunicella labiata	++	+	+	+	+	No
EL62	Vibrio sp.	Eunicella labiata	+	+	+	+	+	No
EL67	Vibrio sp.	Eunicella labiata	+	++	+	+	+	No
EL112	Vibrio sp.	Eunicella labiata	++	+	+	+	+	No
Vb255	Vibrio sp.	Sarcotragus spinosulus	++	+	++	+	+	Yes^e
Vb258	Vibrio sp.	Sarcotragus spinosulus	++	+	++	+	+	Yes^f
Vb341	Vibrio sp.	Sarcotragus spinosulus	+	+	+	+	-	No
Vb339	Vibrio sp.	Sarcotragus spinosulus	+	+	+	+	+	GCA_902751245.1
Vb278	Vibrio sp.	Sarcotragus spinosulus	++	++	+	+	+	CVNE00000000.1
Cw315	Colwellia sp.	Sarcotragus spinosulus	−	−	+	−	−	No
Pa284	Pseudoalteromonas sp.	Sarcotragus spinosulus	+	+	++	−	−	No
EL12	Shewanella sp.	Eunicella labiata	−	+	++	+	−	No
Sw66	Shewanella sp.	Sarcotragus spinosulus	+	+	+	++	−	No
Mb45	Microbulbifer sp.	Sarcotragus spinosulus	++	+	+	+	−	No
EL27	Pseudophaeobacter sp.	Eunicella labiata	−	−	−	−	−	OMPQ00000000.1
EL26	Roseovarius sp.	Eunicella labiata	−	−	−	−	−	OUMZ00000000.1
EL01	Ruegeria sp.	Eunicella labiata	−	−	−	−	−	OMPS00000000.1
Rg50	Ruegeria sp.	Sarcotragus spinosulus	−	−	+	−	−	No
EL44	Sulfitobacter sp.	Eunicella labiata	−	−	−	−	−	OMPT00000000.1
EL53	uncl. Rhodobacteraceae	Eunicella labiata	−	−	+	−	−	OMPR00000000.1
EL129	uncl. Rhodobacteraceae	Eunicella labiata	−	−	−	−	−	ONZJ00000000.1
Ph222	uncl. Rhodobacteraceae	Ircinia variabilis	−	−	−	−	−	No
EL143	Labrenzia alba	Eunicella labiata	−	+	+	−	−	OGUZ00000000.1
Pv125	Pseudovibrio sp.	Sarcotragus spinosulus	−	−	++	−	−	No
EL199	Kiloniella sp.	Eunicella labiata	−	−	+	+	−	OMPU00000000.1
EL138	Sphingorhabdus sp.	Eunicella labiata	−	−	−	−	−	OGVD00000000.1

^aEunicella labiata: octocoral; Sarcotragus spinosulus and Ircinia variabilis: marine sponges
^bChitin degradation observed as halo formation on colloidal chitin-containing agar plates: ++ halo-radius ≥ 8 mm, + halo-radius ≥ 1 mm and < 8 mm
^cChitinase activity measured in Units/ml on bacterial culture supernatants (EndoS3 = endo-chitinase activity) or cell extracts (ExoS1 = exo-chitinase β-N-acetylglucosaminidase activity; ExoS2 = exo-chitinase chitobiosidase activity): ++ ≥ 1 U/mL, + ≥ 0.01 and < 1 U/mL
^dPCR-based amplification of the chiA gene fragments. ^eAccession numbers are provided for genome sequences available on NCBI
^e,fUnpublished draft genomes

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ISSN: 2049-2618

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