一部の古細菌は光エネルギーの利用も行うようである。バクテリオクロロフィルを使った光合成は知られていないものの[注 24]、高度好塩菌やMarine group IIが保有する、バクテリオロドプシンやプロテオロドプシンは、光駆動プロトンポンプの機能を持つ[118][119]。地球上における光エネルギーの利用はバクテリオクロロフィルを含むクロロフィル型が主だと考えられてきたが、細菌を含めたプロテオロドプシンによるエネルギー生産量はその1割にも達すると見積もられており[120]、古細菌Marine group IIもその一部を占める。ただしこれらは炭素固定を行わない光従属栄養生物と考えられる。
左:3ドメイン説、右:エオサイト説。EF-1のインデルの比較ではエオサイト説が支持される[162][注 29]。29遺伝子と化石証拠に基づく系統樹(Holly C. Betts et al., 2018[157])の概観。この系統樹では2分岐説が採用されている。主要系統以外は省略。古細菌の中では最初に分岐したDPANN系統や、コル古細菌などは省略した。
^Ferroplasma acidarmanusとFerroplasma type II(16S rRNA配列99.2%)の間にも組み換えは起こるが、Ferroplasma acidarmanus同士よりもはるかに少ない組み換えしか見られない
^1例のみだが、未培養系統の古細菌MCG-A(Bathyarchaeota class 6)からバクテリオクロロフィルa合成酵素を含む配列が報告されている[14]。このar-bchG(古細菌型バクテリオクロロフィルa合成酵素)は、細菌の持つバクテリオクロロフィルa合成酵素とは系統的に離れており、最も同一性の高いRhodospirillum rubrumとの比較でも27%しか一致しない。大腸菌で発現させた実験によると、実際にこの遺伝子は機能するようである。
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Boone, D. R., Castenholz, R. W. & Garrity, G. M. (2001). Bergey's Manual of Systematic Bacteriology, 2nd Edition, Volume One,The Archaea and the Deeply Branching and Phototrophic Bacteria. Springer-Verlag. ISBN 0387987711