In­te­gra­ti­ve mi­kro­bi­el­le Ge­no­mik

Comparing genomes recovered from time-series metagenomes using long-and short-read sequencing technologies

We com­pa­red me­ta­ge­no­me-as­sem­bled ge­no­mes (MAGs) of the same spe­cies using short- (SR) and long-read (LR) se­quen­cing re­co­ve­r­ed from the sam­ples. As ex­pec­ted, LR MAGs were less frag­men­ted and slight­ly lon­ger than tho­se re­co­ve­r­ed from SR me­ta­ge­no­mic sam­ples. Most im­port­ant­ly, 89% LR MAGs car­ri­ed a full-length 16S rRNA (only 23% in SR MGs). We also found uni­que spe­cies re­co­ve­r­ed using each tech­no­lo­gy. When we ex­ami­ned the pre­sence of the­se uni­que MAGs in the op­po­si­te se­quen­cing tech­no­lo­gy, they had low se­quen­cing depth and low bre­adth of co­ver­age. In­te­res­ting­ly, the­se uni­que spe­cies had a GC bias de­pen­ding on the se­quen­cing plat­form used: uni­que spe­cies in LR had hig­her GC, whe­re­as and tho­se re­co­ve­r­ed from SR had lo­wer GC. Over­all, this work high­lights the be­ne­fits and pit­falls when using SR and LR tech­no­lo­gies to re­co­ver MAGs from en­vi­ron­men­tal sam­ples.

Verrucomicrobiota are specialist consumers of sulfated methyl pentoses during diatom blooms

Mem­bers of the phyl­um Verrucomicrobiota are enig­ma­tic, of­ten un­der­stu­di­ed, and un­der­re­pre­sen­ted in da­ta­ba­ses. No­nethe­l­ess, their pre­sence in dif­fe­rent en­vi­ron­ments, from the oce­an to the gut, re­flects, for the mo­ment, an un­told evo­lu­tio­na­ry his­to­ry of ad­ap­ta­ti­ons and spe­cia­liza­t­i­on events.

Un­li­ke other he­te­ro­tro­phic bac­te­ria from the spring blooms, Verrucomicrobiota cells are well equip­ped to de­gra­de high­ly sul­fa­ted po­ly­sac­cha­ri­des con­tai­ning fu­co­se and rham­no­se. Using me­ta­ge­no­mics, me­ta­pro­teo­mics, and cell vi­sua­liza­t­i­on ap­proa­ches, we found that Verrucomicrobiota use a com­bi­na­ti­on of spe­cia­li­zed pa­thways for fu­co­se de­gra­da­ti­on that, com­ple­men­ted with bac­te­ri­al mi­cro­com­part­ments, can avo­id the ac­cu­mu­la­ti­on of to­xic in­ter­me­dia­tes.

Sup­po­se you were to com­pa­re the me­ta­bo­lic po­ten­ti­al light­ly: Verrucomicrobiota po­pu­la­ti­ons and pro­li­fic he­te­ro­tro­phs, such as mem­bers of the phyl­um Bacteroidota, have an equi­va­lent num­ber of sul­fa­tes and gly­co­si­de hy­dro­la­se ge­nes for po­ly­sac­cha­ri­de de­gra­da­ti­on. Howe­ver, it’s more than just num­bers: Most Ver­ru­co­mi­cro­bio­ta cells car­ry spe­cia­li­zed de­gra­da­ti­on pa­thways that, lin­ked to bac­te­ri­al mi­cro­com­part­ments, can cir­cum­vent the ac­cu­mu­la­ti­on of the to­xic lac­tal­de­hy­de. No other group in the bloom unites such spe­cia­li­zed me­cha­nisms for the de­gra­da­ti­on of fu­co­se and rham­no­se.

Com­bi­ning me­ta­ge­no­mic ap­proa­ches with CARD-FISH also al­lo­wed us to name two re­pre­sen­ta­ti­ve spe­cies as Candidatus Ma­riak­ker­m­an­sia for­se­tii and Candidatus Fu­ci­vor­ax for­se­tii. It seems you CAN make a li­ving being pi­cky (and spe­cia­li­zed) at what you eat, or at least du­ring the spring blooms.

Niche differentiation among annually recurrent coastal Marine Group II  Euryarchaeota

We com­bi­ned me­ta­ge­no­mic and vi­sua­liza­t­i­on ap­proa­ches to ex­plo­re the Eu­ry­ar­chaeo­ta MGIIa and MGI­Ib po­pu­la­ti­ons' tem­po­ral dis­tri­bu­ti­on in the North Sea. The com­bi­na­ti­on of oli­go­typ­ing and FISH ap­proa­ches re­vea­led that MGII cells were most­ly free-li­ving and of a small coc­co­id shape, li­kely re­sul­ting in gra­zing avo­idance. Our me­ta­ge­no­mic ap­proach al­lo­wed us to re­co­ver MAGs that re­vea­led dif­fe­ren­ces in the ge­no­me size and GC con­tent bet­ween MGIIa and MGI­Ib. Ad­di­tio­nal­ly, we ob­ser­ved high­ly iden­ti­cal and an­nu­al­ly re­cur­rent dis­cre­te po­pu­la­ti­ons for both fa­mi­lies du­ring the win­ter and sum­mer pe­ri­ods hy­po­the­si­ze that a com­bi­na­ti­on of size and me­ta­bo­lic po­ten­ti­al de­linea­tes MGII po­pu­la­ti­ons' ni­ches. Read more about it in the "be­hind the pa­per" blog post.

Read the paper