Peeling off the layers from microbial dark matter (MDM): recent advances, future challenges, and opportunities

Figures & data

Figure 1. Timeline showing advances in culture-dependent (a) and culture-independent (b) approaches to study microbial dark matter (MDM).

Figure 2. Schematic workflow used to generate SAGs and MAGs. Single-cell is physically separated from a complex environmental sample using microfluidics, flow cytometry, or a single-cell printer. Various genome binning tools are freely available, including MetaBAT (Kang et al. 2019), MaxBin (Wu et al. 2016), and CONCOCT (Alneberg et al. 2014). The quality of the draft genome is checked using CheckM or MDMcleaner and should follow the criteria for SAGs/MAGs suggested by the genome standard consortium (Bowers et al. 2017).

Table 1. Novel candidate prokaryotic phyla discovered through SAGs/MAGs.

Phylum name	MAG/SAG	Sample source	Country	Reference
Altiarchaeota	MAG	Estuary sediments	USA	(Seitz et al. 2016)
Bathyarchaeota	MAG	Qi’ao Island	China	(Meng et al. 2014)
Binatota	MAG	Unknown	Public databases	(Chuvochina et al. 2019)
Blackallbacteria	MAG	Deep terrestrial subsurface	USA	(Probst et al. 2018)
Brockarchaeota	MAG	Hot spring	China	(De Anda et al. 2021)
Caldatribacteriota	MAG	Hydrothermal sediments	USA	(Hahn et al. 2020)
Desantisbacteria	MAG	Crystal Geyser	USA	(Probst et al. 2017)
Eremiobacterota (WPS-2)	MAG	Not applicable	Public databases	(Ward et al. 2019)
Genascibacteria	MAG	Groundwater	USA	(He et al. 2021)
Geothermarchaeota	MAG	Hydrothermal Subsurface fluid	USA	(Jungbluth et al. 2017)
Gribaldobacteria	MAG	CO2-driven geyser	USA	(Probst et al. 2018)
Hadarchaeota	MAG	Not applicable	Public database	(Chuvochina et al. 2019)
Hadesarchaeota	MAG	Shallow salt Sediments	USA	(McGonigle et al. 2019)
Halobacterota	MAG	Not applicable	Public database	(L Bräuer et al. 2020)
Hydrothermota	MAG	Not applicable	Public database	(Chuvochina et al. 2019)
Sifarchaeota	MAG	Costal Rican sediments	USA	(Farag et al. 2021)
Dependentiae (TM6 revised)	MAG	Chiba	Japan	(Takemura 2022)
Lokiarchaeia	MAG	Microoxic lake	Romania	(Bulzu et al. 2019)
Micrarchaeota	MAG	Unknown	Public database	(Baker and Dick 2013)
Modulibacteria	MAG	Methanogenic sludge	Australia	(Sekiguchi et al. 2015)
Moisslbacteria	MAG	CO2-driven geyser	USA	(Probst et al. 2018)
Montesolbacteria	MAG	Ground water	USA	(He et al. 2021)
Ratteibacteria	MAG	CO2-driven geyser	USA	(Probst et al. 2018)
Thermoplasmatota	MAG	Sea water	Australia	(Rinke et al. 2019)
Tianyabacteria	MAG	Deep sea sediment	Federated states of Micronesia	(Cui et al. 2021)
Torokbacteria	MAG	CO2-driven geyser	USA	(Probst et al. 2018)
Wirthbacteria	Both	Unknown	Genome Institute’s IMG database	(Hug et al. 2016)
Zixibacteria	MAG	Aquifer sediment	USA	(Castelle et al. 2013)
Abawacabacteria	MAG	Suboxic/anoxic aquifer	USA	(Anantharaman et al. 2016)
Aminanaerobia	MAG	Termite gut	Costa Rica	(Warnecke et al. 2007)
Asgardarchaeota	MAG	Unknown	ATGT database	(Rinke et al. 2021)
Aureabacteria	MAG	Gold mine deep terrestrial subsurface	USA	(Momper et al. 2017)
Auribacterota	MAG	Antarctic lake		(Williams et al. 2022)
Baldrarchaeota	MAG	Rongcheng Swan Lake	China	(Liu Y et al. 2021)
Borrarchaeota	MAG	Rongcheng Swan Lake	China	(Liu Y et al. 2021)
Canglongiota	MAG	Yap trench	China	(Zhang X et al. 2022)
Cloacimonadota	MAG	Antarctic lake	Antarctica	(Williams et al. 2022)
Deferrimicrobiota	MAG	Boreal peatland	USA	(Begmatov et al. 2022)
Electryoneota	MAG	Antarctic lake	Antarctica	(Williams et al. 2022)
Freyrarchaeota	MAG	Rongcheng Swan Lake	China	(Xie et al. 2022)
Gerdarchaeota	MAG	Coastal mud and sediments	China	(Cai et al. 2020)
Heilongiota	MAG	Tap trench	China	(Zhang X et al. 2022)
Hermodarchaeota	MAG		China	(Liu Y et al. 2021)
Hinthialibacterota	MAG	Antarctic lake	Antarctica	(Williams et al. 2022)
Hodarchaeota	MAG	Antarctic lake	Antarctica	(Williams et al. 2022)
Kapaibacteria	MAG	Bioreactor ecosystem	USA	(Kantor et al. 2015)
Kariarchaeota	MAG	Rongcheng Swan Lake	China	(Liu Y et al. 2021)
Lernaellota	MAG			(Williams et al. 2022)
Lithacetigenota	MAG	Hakuba Happo hot spring	Japan	(Nobu et al. 2023)
Njordarchaeota	MAG	Rongcheng Swan Lake	China	(Xie et al. 2022)
Omnitrophota	MAG	Antarctic lake	Antarctica	(Williams et al. 2021)
Qinglongiota	MAG	Yap trench	China	(Zhang X et al. 2022)
Sigynarchaeota	MAG	Rongcheng Swan Lake	China	(Xie et al. 2022)
Thorarchaeia	MAG	Microoxic nich	Romania	(Bulzu et al. 2019)
Wukongarchaeota	MAG	Rongcheng Swan Lake	China	(Liu Y et al. 2021)

Figure 3. Schematic representation of microbial dark matter (MDM) research progress and future opportunities.

Figure 4. Application of microbial dark matter (MDM) in various fields.

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